Keniajin authored on 18/11/2022 14:31:48
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@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: protGear |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Protein Micro Array Data Management and Interactive Visualization |
| 4 |
-Version: 1.3.0 |
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+Version: 1.2.1 |
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| 5 | 5 |
Authors@R: c(person("Kennedy", "Mwai", role = c("cre", "aut"), email = "keniajin@gmail.com"),
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| 6 | 6 |
person(c("James", "Mburu"), role = "aut" , email = "mburuwanja@gmail.com") ,
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| 7 | 7 |
person(c("Jacqueline", "Waeni"), role = "ctb" , email = "jacqwaeni@gmail.com"))
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| ... | ... |
@@ -481,25 +481,20 @@ plot_FB <- |
| 481 | 481 |
#' @import dplyr limma |
| 482 | 482 |
#' @importFrom rlang sym |
| 483 | 483 |
#' @examples |
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-#' ## Not run: |
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+#' ## Not Run |
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| 485 | 485 |
#' genepix_vars <- array_vars( |
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-#' channel = "635", |
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-#' chip_path = system.file("extdata", "array_data/machine1/",
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-#' package="protGear"), |
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+#' channel = '635', |
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+#' chip_path = system.file('extdata', 'array_data/machine1/',
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+#' package='protGear'), |
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| 489 | 489 |
#' totsamples = 21, |
| 490 | 490 |
#' blockspersample = 2, |
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-#' mig_prefix = "_first", |
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+#' mig_prefix = '_first', |
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| 492 | 492 |
#' machine = 1, |
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-#' ## optional |
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-#' date_process = "0520" |
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-#' ) |
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-#' raw_df <- readr::read_csv(system.file("extdata", "Data1_bg_sample.csv",
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-#' package="protGear")) |
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-#' bg_correct(iden="iden", |
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-#' Data1 = raw_df, |
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-#' genepix_vars = genepix_vars, method="subtract_local" |
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-#' ) |
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-#' ## End(Not run) |
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+#' date_process = '0520') |
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+#' raw_df <- readr::read_csv(system.file('extdata','Data1_bg_sample.csv',
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+#' package='protGear')) |
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+#' bg_correct(iden='iden', Data1 = raw_df, genepix_vars = genepix_vars, |
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+#' method='subtract_local') |
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| 503 | 498 |
bg_correct <- |
| 504 | 499 |
function(iden, Data1, genepix_vars, method = "subtract_local") {
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| 505 | 500 |
#-------------------------------------------------------------------------- |
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new file mode 100644 |
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+<!DOCTYPE html> |
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"> |
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+<head> |
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+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> |
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+<meta charset="utf-8"> |
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+<meta http-equiv="X-UA-Compatible" content="IE=edge"> |
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+<meta name="viewport" content="width=device-width, initial-scale=1.0"> |
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+<title>Page not found (404) • protGear</title> |
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+<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"> |
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+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="bootstrap-toc.css"> |
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+<script src="bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"> |
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+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"> |
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+<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"> |
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+<script src="pkgdown.js"></script><meta property="og:title" content="Page not found (404)"> |
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+<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> |
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+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> |
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+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> |
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+<![endif]--> |
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+</head> |
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+<body data-spy="scroll" data-target="#toc"> |
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+ |
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+ |
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+ <div class="container template-title-body"> |
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+ <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> |
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+ <div class="container"> |
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+ <div class="navbar-header"> |
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+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> |
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+ <span class="sr-only">Toggle navigation</span> |
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+ <span class="icon-bar"></span> |
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+ <span class="icon-bar"></span> |
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+ <span class="icon-bar"></span> |
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+ </button> |
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+ <span class="navbar-brand"> |
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+ <a class="navbar-link" href="index.html">protGear</a> |
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+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.2.1</span> |
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+ <div id="navbar" class="navbar-collapse collapse"> |
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+ <ul class="nav navbar-nav"> |
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+<li class="dropdown"> |
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+ Articles |
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+ <span class="caret"></span> |
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+ </a> |
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+ <ul class="dropdown-menu" role="menu"> |
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+<li> |
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+ <a href="articles/vignette.html">protGear vignette processing suite</a> |
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+ </li> |
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+ </ul> |
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+</li> |
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+<li> |
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+ <a href="news/index.html">Changelog</a> |
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+</li> |
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+ </ul> |
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+<ul class="nav navbar-nav navbar-right"> |
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+<li> |
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+ <a href="https://github.com/Keniajin/protGear/" class="external-link"> |
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+ <span class="fab fa-github fa-lg"></span> |
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+ </a> |
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+</li> |
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+ </ul> |
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+</div> |
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+<!--/.nav-collapse --> |
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+<!--/.navbar --> |
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+ </header><div class="row"> |
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+ <div class="contents col-md-9"> |
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+ <div class="page-header"> |
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+ <h1>Page not found (404)</h1> |
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+ </div> |
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+ |
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+Content not found. Please use links in the navbar. |
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+ |
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+ </div> |
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+ |
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+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |
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+ <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> |
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+ </nav> |
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+</div> |
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+</div> |
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+ |
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+ <footer><div class="copyright"> |
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+ <p></p> |
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+<p>Developed by Kennedy Mwai, James Mburu.</p> |
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+</div> |
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+ |
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+<div class="pkgdown"> |
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+ <p></p> |
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+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> |
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+</div> |
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+ </footer> |
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+ </body> |
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+</html> |
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new file mode 100644 |
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+<!DOCTYPE html> |
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Articles • protGear</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Articles"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> |
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+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> |
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+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> |
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+<![endif]--></head><body data-spy="scroll" data-target="#toc"> |
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+ |
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+ <div class="container template-article-index"> |
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+ <div class="navbar-header"> |
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+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> |
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+ <span class="sr-only">Toggle navigation</span> |
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+ <span class="icon-bar"></span> |
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+ <span class="icon-bar"></span> |
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+ <span class="icon-bar"></span> |
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+ </button> |
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+ <span class="navbar-brand"> |
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+ <a class="navbar-link" href="../index.html">protGear</a> |
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+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.2.1</span> |
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+ </span> |
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+ </div> |
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+ |
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+ <div id="navbar" class="navbar-collapse collapse"> |
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+ <ul class="nav navbar-nav"><li> |
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+ <a href="../reference/index.html">Reference</a> |
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+</li> |
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+<li class="dropdown"> |
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+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> |
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+ Articles |
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+ <span class="caret"></span> |
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+ </a> |
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+ <ul class="dropdown-menu" role="menu"><li> |
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+ <a href="../articles/vignette.html">protGear vignette processing suite</a> |
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+ </li> |
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| 37 |
+ </ul></li> |
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| 38 |
+<li> |
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+ <a href="../news/index.html">Changelog</a> |
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+</li> |
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+ </ul><ul class="nav navbar-nav navbar-right"><li> |
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+ <a href="https://github.com/Keniajin/protGear/" class="external-link"> |
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+ <span class="fab fa-github fa-lg"></span> |
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+ |
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+ </a> |
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+</li> |
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+ </ul></div><!--/.nav-collapse --> |
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+ </div><!--/.container --> |
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+</div><!--/.navbar --> |
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+ |
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+ |
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+ |
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+ </header><div class="row"> |
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+ <div class="col-md-9 contents"> |
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+ <div class="page-header"> |
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+ <h1>Articles</h1> |
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+ </div> |
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+ |
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+ <div class="section "> |
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+ <h3>All vignettes</h3> |
|
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+ <p class="section-desc"></p> |
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+ |
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+ <dl><dt><a href="vignette.html">protGear vignette processing suite</a></dt> |
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+ <dd> |
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+ </dd></dl></div> |
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+ </div> |
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+</div> |
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+ |
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+ |
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+ <footer><div class="copyright"> |
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+ <p></p><p>Developed by Kennedy Mwai, James Mburu.</p> |
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+</div> |
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+ |
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+<div class="pkgdown"> |
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+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> |
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+ </footer></div> |
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+ |
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+ </body></html> |
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+ |
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new file mode 100644 |
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+<!DOCTYPE html> |
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"> |
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+<head> |
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+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> |
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+<meta charset="utf-8"> |
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+<meta http-equiv="X-UA-Compatible" content="IE=edge"> |
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+<meta name="viewport" content="width=device-width, initial-scale=1.0"> |
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+<title>protGear vignette processing suite • protGear</title> |
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+<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"> |
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+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"> |
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+<script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"> |
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+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"> |
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+<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> |
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+<script src="../pkgdown.js"></script><meta property="og:title" content="protGear vignette processing suite"> |
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+ <a href="../articles/vignette.html">protGear vignette processing suite</a> |
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+ |
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+ |
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+ </header><script src="vignette_files/kePrint-0.0.1/kePrint.js"></script><link href="vignette_files/lightable-0.0.1/lightable.css" rel="stylesheet"> |
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+ <div class="col-md-9 contents"> |
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+ <div class="page-header toc-ignore"> |
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+ <h1 data-toc-skip>protGear vignette processing suite</h1> |
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+ <h4 data-toc-skip class="author">Kennedy |
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+Mwai</h4> |
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+ |
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+ <h4 data-toc-skip class="date">18 November, 2022</h4> |
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+ |
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+ <small class="dont-index">Source: <a href="https://github.com/Keniajin/protGear/blob/HEAD/vignettes/vignette.Rmd" class="external-link"><code>vignettes/vignette.Rmd</code></a></small> |
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+ <div class="hidden name"><code>vignette.Rmd</code></div> |
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+ |
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+ </div> |
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+ |
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+ |
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+ |
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+<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> |
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+<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://rpkgs.datanovia.com/ggpubr/" class="external-link">ggpubr</a></span><span class="op">)</span></span> |
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+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/r-gregmisc/gtools" class="external-link">gtools</a></span><span class="op">)</span></span> |
|
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+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://purrr.tidyverse.org/" class="external-link">purrr</a></span><span class="op">)</span></span> |
|
| 99 |
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://scales.r-lib.org" class="external-link">scales</a></span><span class="op">)</span></span> |
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+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">pheatmap</span><span class="op">)</span></span> |
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+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://r-datatable.com" class="external-link">data.table</a></span><span class="op">)</span></span> |
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+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="http://haozhu233.github.io/kableExtra/" class="external-link">kableExtra</a></span><span class="op">)</span></span> |
|
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+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">gridExtra</span><span class="op">)</span></span> |
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+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="http://www.rforge.net/png/" class="external-link">png</a></span><span class="op">)</span></span> |
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+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://yihui.org/knitr/" class="external-link">knitr</a></span><span class="op">)</span></span> |
|
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+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">grid</span><span class="op">)</span></span> |
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+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/r-lib/styler" class="external-link">styler</a></span><span class="op">)</span></span> |
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| 108 |
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="http://factominer.free.fr" class="external-link">FactoMineR</a></span><span class="op">)</span></span> |
|
| 109 |
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="http://www.sthda.com/english/rpkgs/factoextra" class="external-link">factoextra</a></span><span class="op">)</span></span> |
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+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://docs.ropensci.org/magick/" class="external-link">magick</a></span><span class="op">)</span></span> |
|
| 111 |
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://rlang.r-lib.org" class="external-link">rlang</a></span><span class="op">)</span></span> |
|
| 112 |
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggobi.github.io/ggally/" class="external-link">GGally</a></span><span class="op">)</span></span> |
|
| 113 |
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/GuangchuangYu/ggplotify" class="external-link">ggplotify</a></span><span class="op">)</span></span> |
|
| 114 |
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://remotes.r-lib.org" class="external-link">remotes</a></span><span class="op">)</span></span> |
|
| 115 |
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span> |
|
| 116 |
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://tidyr.tidyverse.org" class="external-link">tidyr</a></span><span class="op">)</span></span> |
|
| 117 |
+<span><span class="fu">knitr</span><span class="fu">::</span><span class="va"><a href="https://rdrr.io/pkg/knitr/man/opts_chunk.html" class="external-link">opts_chunk</a></span><span class="op">$</span><span class="fu">set</span><span class="op">(</span>echo <span class="op">=</span> <span class="cn">TRUE</span>, message<span class="op">=</span><span class="cn">FALSE</span>,warning <span class="op">=</span> <span class="cn">FALSE</span>,</span> |
|
| 118 |
+<span> fig.align <span class="op">=</span> <span class="st">'center'</span>,</span> |
|
| 119 |
+<span> dev <span class="op">=</span> <span class="st">"png"</span>, </span> |
|
| 120 |
+<span> tidy<span class="op">=</span><span class="st">'styler'</span>, tidy.opts<span class="op">=</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>strict<span class="op">=</span><span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> |
|
| 121 |
+<style type="text/css"> |
|
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+.custom-inline {
|
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+ color: red; |
|
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+ font-weight: 700 |
|
| 125 |
+} |
|
| 126 |
+</style> |
|
| 127 |
+<div class="section level2"> |
|
| 128 |
+<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a> |
|
| 129 |
+</h2> |
|
| 130 |
+<div class="section level3"> |
|
| 131 |
+<h3 id="general-information">General information<a class="anchor" aria-label="anchor" href="#general-information"></a> |
|
| 132 |
+</h3> |
|
| 133 |
+<p>protGear is a package for protein micro data processing just before |
|
| 134 |
+the main analysis. The package loads the ‘<code>gpr</code>’ or |
|
| 135 |
+‘<code>txt</code>’ file format extracted by the quantification software |
|
| 136 |
+and merges this with the specific sample identifiers. The package |
|
| 137 |
+processes multiple files extracted batch by batch with their |
|
| 138 |
+corresponding sample identifier file. The sample identifier file has 2 |
|
| 139 |
+variables ‘<code>v1</code>’ and ‘<code>v2</code>’ which indicate the |
|
| 140 |
+mini-array or block number and sample identifier respectively. The |
|
| 141 |
+‘<code>gpr</code>’ file and the corresponding sample identifier file |
|
| 142 |
+have the same file name. protGear also provides a web based <span class="math inline">\(Shiny^{(R)}\)</span> platform for real time
|
|
| 143 |
+visualization of the data processing.</p> |
|
| 144 |
+<p>In this vignette the general work-flow of protGear will be outlined |
|
| 145 |
+by processing a sample dataset from a multicentre study |
|
| 146 |
+<strong>Plasmodium falciparum</strong> Merozoite Protein Microarray. The |
|
| 147 |
+multicentre study design motivated the development of the protGear |
|
| 148 |
+suite.</p> |
|
| 149 |
+<p>The details of the methodologies are published here <a href="https://doi.org/10.1016/j.csbj.2021.04.044" class="external-link uri">https://doi.org/10.1016/j.csbj.2021.04.044</a></p> |
|
| 150 |
+</div> |
|
| 151 |
+<div class="section level3"> |
|
| 152 |
+<h3 id="analysis-setup">Analysis setup<a class="anchor" aria-label="anchor" href="#analysis-setup"></a> |
|
| 153 |
+</h3> |
|
| 154 |
+<p>Create 2 folders that hold the ‘<code>.gpr</code>’ files and the |
|
| 155 |
+corresponding sample identifier files.</p> |
|
| 156 |
+<div class="figure"> |
|
| 157 |
+<img src="folder_structure.png" style="width:70.0%" alt=""><p class="caption">Folder structure of array and sample ID files</p> |
|
| 158 |
+</div> |
|
| 159 |
+</div> |
|
| 160 |
+</div> |
|
| 161 |
+<div class="section level2"> |
|
| 162 |
+<h2 id="sample-identifier-file">Sample identifier file<a class="anchor" aria-label="anchor" href="#sample-identifier-file"></a> |
|
| 163 |
+</h2> |
|
| 164 |
+<div class="figure"> |
|
| 165 |
+<img src="image_slide.png" alt=""><p class="caption">sample ID file structure</p> |
|
| 166 |
+</div> |
|
| 167 |
+<div class="section level3"> |
|
| 168 |
+<h3 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a> |
|
| 169 |
+</h3> |
|
| 170 |
+<p>To install <code>protGear</code> from BioConductor the following |
|
| 171 |
+commands in R</p> |
|
| 172 |
+<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> |
|
| 173 |
+<code class="sourceCode R"><span><span class="co">## install from BioConductor</span></span> |
|
| 174 |
+<span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st">"BiocManager"</span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span>
|
|
| 175 |
+<span> <span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"BiocManager"</span><span class="op">)</span></span> |
|
| 176 |
+<span><span class="op">}</span></span> |
|
| 177 |
+<span><span class="fu">BiocManager</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/BiocManager/man/install.html" class="external-link">install</a></span><span class="op">(</span><span class="st">"protGear"</span><span class="op">)</span></span></code></pre></div> |
|
| 178 |
+</div> |
|
| 179 |
+</div> |
|
| 180 |
+<div class="section level2"> |
|
| 181 |
+<h2 id="importing-data">Importing data<a class="anchor" aria-label="anchor" href="#importing-data"></a> |
|
| 182 |
+</h2> |
|
| 183 |
+<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> |
|
| 184 |
+<code class="sourceCode R"><span><span class="co">## load the package</span></span> |
|
| 185 |
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/Keniajin/protGear" class="external-link">protGear</a></span><span class="op">)</span></span></code></pre></div> |
|
| 186 |
+<p>The first part is to specify the parameters of the micro-array |
|
| 187 |
+experiment to assist in processing the data. The parameters specified |
|
| 188 |
+are</p> |
|
| 189 |
+<ul> |
|
| 190 |
+<li>channel - The scanner fluorescence output used to record the data. |
|
| 191 |
+It can be green,red,blue among others with a specified number.</li> |
|
| 192 |
+<li>chip_path - the folder where the sub folders of ‘gpr’ or ‘txt’ files |
|
| 193 |
+are stored. This path contains sub folders with the array data, for |
|
| 194 |
+example the sub folders for the different batches.</li> |
|
| 195 |
+<li>totsamples - the number of samples in a slide or array.<br> |
|
| 196 |
+</li> |
|
| 197 |
+<li>blockspersample - The number of blocks a sample it takes. In this |
|
| 198 |
+example each sample occupies 2 blocks each with 384 spots.</li> |
|
| 199 |
+<li>sampleID_path - the folder where the sample identifiers files are |
|
| 200 |
+stored</li> |
|
| 201 |
+<li>machine - The indicator for which machine was used to hybridize the |
|
| 202 |
+samples if the experiment had more than one machine.</li> |
|
| 203 |
+<li>date_process -the date of sample processing</li> |
|
| 204 |
+</ul> |
|
| 205 |
+<p>The parameters “<code>chip_path</code>”, “<code>channel</code>” , |
|
| 206 |
+“<code>totsamples</code>” and “<code>sampleID_path</code>” are |
|
| 207 |
+mandatory.</p> |
|
| 208 |
+<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> |
|
| 209 |
+<code class="sourceCode R"><span><span class="co">## specify the the parameters to process the data</span></span> |
|
| 210 |
+<span><span class="va">genepix_vars</span> <span class="op"><-</span> <span class="fu"><a href="../reference/array_vars.html">array_vars</a></span><span class="op">(</span></span> |
|
| 211 |
+<span> channel <span class="op">=</span> <span class="st">"635"</span>,</span> |
|
| 212 |
+<span> chip_path <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata/array_data/"</span>, package <span class="op">=</span> <span class="st">"protGear"</span><span class="op">)</span>,</span> |
|
| 213 |
+<span> totsamples <span class="op">=</span> <span class="fl">21</span>,</span> |
|
| 214 |
+<span> blockspersample <span class="op">=</span> <span class="fl">2</span>,</span> |
|
| 215 |
+<span> sampleID_path <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata/array_sampleID/"</span>, package <span class="op">=</span> <span class="st">"protGear"</span><span class="op">)</span>,</span> |
|
| 216 |
+<span> mig_prefix <span class="op">=</span> <span class="st">"_first"</span>,</span> |
|
| 217 |
+<span> machine <span class="op">=</span> <span class="fl">1</span>,</span> |
|
| 218 |
+<span> <span class="co">## optional</span></span> |
|
| 219 |
+<span> date_process <span class="op">=</span> <span class="st">"0520"</span></span> |
|
| 220 |
+<span><span class="op">)</span></span></code></pre></div> |
|
| 221 |
+<p>The exact channel used should be checked in the header of the file |
|
| 222 |
+from the quantification software under <code>Wavelengths</code>.</p> |
|
| 223 |
+<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> |
|
| 224 |
+<code class="sourceCode R"><span><span class="va">header_gpr</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/readLines.html" class="external-link">readLines</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata/array_data/machine1/KK2-06.txt"</span>, package <span class="op">=</span> <span class="st">"protGear"</span><span class="op">)</span>,</span> |
|
| 225 |
+<span> n <span class="op">=</span> <span class="fl">40</span></span> |
|
| 226 |
+<span><span class="op">)</span></span> |
|
| 227 |
+<span><span class="va">header_gpr</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/grep.html" class="external-link">gsub</a></span><span class="op">(</span><span class="st">"\""</span>, <span class="st">""</span>, <span class="va">header_gpr</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">32</span><span class="op">]</span><span class="op">)</span></span> |
|
| 228 |
+<span><span class="va">header_gpr</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">32</span><span class="op">]</span></span></code></pre></div> |
|
| 229 |
+<pre><code><span><span class="co">## [1] "ATF\t1\t\t\t\t\t\t\t\t\t\t\t\t\t\t" </span></span> |
|
| 230 |
+<span><span class="co">## [2] "29\t31\t\t\t\t\t\t\t\t\t\t\t\t\t\t" </span></span> |
|
| 231 |
+<span><span class="co">## [3] "Type=GenePix Export 3\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t" </span></span> |
|
| 232 |
+<span><span class="co">## [4] "DateTime=2017/09/05 17:17:47\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t" </span></span> |
|
| 233 |
+<span><span class="co">## [5] "Settings=\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t" </span></span> |
|
| 234 |
+<span><span class="co">## [6] "GalFile=C:\\Users\\rkimathi\\Desktop\\GAL FILE DATA.gal\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t" </span></span> |
|
| 235 |
+<span><span class="co">## [7] "PixelSize=10\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t" </span></span> |
|
| 236 |
+<span><span class="co">## [8] "Wavelengths=635\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t" </span></span> |
|
| 237 |
+<span><span class="co">## [9] "ImageFiles=Z:\\Multicenter study\\4_9_2017\\data\\BRB0001.tif 0\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t" </span></span> |
|
| 238 |
+<span><span class="co">## [10] "NormalizationMethod=None\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t" </span></span> |
|
| 239 |
+<span><span class="co">## [11] "NormalizationFactors=1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t" </span></span> |
|
| 240 |
+<span><span class="co">## [12] "JpegImage=\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t" </span></span> |
|
| 241 |
+<span><span class="co">## [13] "StdDev=Type 1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t" </span></span> |
|
| 242 |
+<span><span class="co">## [14] "FeatureType=Circular\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t" </span></span> |
|
| 243 |
+<span><span class="co">## [15] "Barcode=\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t" </span></span> |
|
| 244 |
+<span><span class="co">## [16] "BackgroundSubtraction=LocalFeature\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t" </span></span> |
|
| 245 |
+<span><span class="co">## [17] "ImageOrigin=0, 0\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t" </span></span> |
|
| 246 |
+<span><span class="co">## [18] "JpegOrigin=1670, 840\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t" </span></span> |
|
| 247 |
+<span><span class="co">## [19] "Creator=GenePix Pro 7.3.0.0\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t" </span></span> |
|
| 248 |
+<span><span class="co">## [20] "Scanner=GenePix 4300 [141110]\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t" </span></span> |
|
| 249 |
+<span><span class="co">## [21] "FocusPosition=0\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t" </span></span> |
|
| 250 |
+<span><span class="co">## [22] "Temperature=0\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t" </span></span> |
|
| 251 |
+<span><span class="co">## [23] "LinesAveraged=1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t" </span></span> |
|
| 252 |
+<span><span class="co">## [24] "Comment=\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t" </span></span> |
|
| 253 |
+<span><span class="co">## [25] "PMTGain=400\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t" </span></span> |
|
| 254 |
+<span><span class="co">## [26] "ScanPower=100\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t" </span></span> |
|
| 255 |
+<span><span class="co">## [27] "LaserPower=0.55\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t" </span></span> |
|
| 256 |
+<span><span class="co">## [28] "Filters=Standard Red\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t" </span></span> |
|
| 257 |
+<span><span class="co">## [29] "ScanRegion=0,0,2200,7200\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t" </span></span> |
|
| 258 |
+<span><span class="co">## [30] "ScanArea=1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t" </span></span> |
|
| 259 |
+<span><span class="co">## [31] "Supplier=\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t" </span></span> |
|
| 260 |
+<span><span class="co">## [32] "Flags\tNormalize\tAutoflag\tBlock\tColumn\tRow\tName\tID\tX\tY\tF635 Median\tB635\tB635 Median\tSNR 635\tF635 Median - B635\tIndex"</span></span></code></pre> |
|
| 261 |
+<p>The function <span style=" color: red !important;">check_sampleID_files()</span> helps |
|
| 262 |
+to check whether each micro array file has a corresponding sample |
|
| 263 |
+identifier file. The sample identifier files are generated from the lab |
|
| 264 |
+plate maps to match the corresponding samples on a specific slide.If the |
|
| 265 |
+sample identifier file is missing, protGear automatically generates the |
|
| 266 |
+id’s.</p> |
|
| 267 |
+<div class="section level3"> |
|
| 268 |
+<h3 id="spatial-structure-of-slide">Spatial structure of slide<a class="anchor" aria-label="anchor" href="#spatial-structure-of-slide"></a> |
|
| 269 |
+</h3> |
|
| 270 |
+<p>protGear offers a functionality to inspect the slide visually for any |
|
| 271 |
+strong spatial biases when the scan image is not available. However, we |
|
| 272 |
+recommend using the scanned image to visualize the spatial artefacts |
|
| 273 |
+that might not be recorded in the <code>.gpr</code> file. We include the |
|
| 274 |
+functions <span style=" color: red !important;">visualize_slide()</span> and <span style=" color: red !important;">visualize_slide_2d()</span> to check |
|
| 275 |
+the spatial structure. The functions are build on <span style=" color: red !important;">structure_plot()</span> which shows |
|
| 276 |
+the block and mini-array structure of a slide.</p> |
|
| 277 |
+<div class="section level4"> |
|
| 278 |
+<h4 id="visualize-the-foreground-mfi">Visualize the foreground MFI<a class="anchor" aria-label="anchor" href="#visualize-the-foreground-mfi"></a> |
|
| 279 |
+</h4> |
|
| 280 |
+<p>Here we visualize the foreground MFI using the <span style=" color: red !important;">visualize_slide</span> function</p> |
|
| 281 |
+<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> |
|
| 282 |
+<code class="sourceCode R"><span><span class="fu"><a href="../reference/visualize_slide.html">visualize_slide</a></span><span class="op">(</span></span> |
|
| 283 |
+<span> infile <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata/array_data/machine1/KK2-06.txt"</span>, package <span class="op">=</span> <span class="st">"protGear"</span><span class="op">)</span>,</span> |
|
| 284 |
+<span> MFI_var <span class="op">=</span> <span class="st">"F635 Median"</span></span> |
|
| 285 |
+<span><span class="op">)</span></span></code></pre></div> |
|
| 286 |
+<p><img src="vignette_files/figure-html/slide_struct-1.png" width="700" style="display: block; margin: auto auto auto 0;"></p> |
|
| 287 |
+</div> |
|
| 288 |
+<div class="section level4"> |
|
| 289 |
+<h4 id="visualize-the-background-mfi">Visualize the background MFI<a class="anchor" aria-label="anchor" href="#visualize-the-background-mfi"></a> |
|
| 290 |
+</h4> |
|
| 291 |
+<p>Here we visualize the background MFI using the |
|
| 292 |
+<code>visualize_slide_2d</code> function</p> |
|
| 293 |
+<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r"> |
|
| 294 |
+<code class="sourceCode R"><span><span class="fu"><a href="../reference/visualize_slide_2d.html">visualize_slide_2d</a></span><span class="op">(</span></span> |
|
| 295 |
+<span> infile <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata/array_data/machine1/KK2-06.txt"</span>, package <span class="op">=</span> <span class="st">"protGear"</span><span class="op">)</span>,</span> |
|
| 296 |
+<span> MFI_var <span class="op">=</span> <span class="st">"B635 Median"</span></span> |
|
| 297 |
+<span><span class="op">)</span></span></code></pre></div> |
|
| 298 |
+<p><img src="vignette_files/figure-html/slide_struct_2d-1.png" width="700" style="display: block; margin: auto auto auto 0;"></p> |
|
| 299 |
+</div> |
|
| 300 |
+</div> |
|
| 301 |
+<div class="section level3"> |
|
| 302 |
+<h3 id="import--gprtxt-data">Import .gpr/txt data<a class="anchor" aria-label="anchor" href="#import--gprtxt-data"></a> |
|
| 303 |
+</h3> |
|
| 304 |
+<p>Microarray data is imported using the <span style=" color: red !important;">read_array_files()</span> function. |
|
| 305 |
+The function accepts the following mandatory arguments;</p> |
|
| 306 |
+<ul> |
|
| 307 |
+<li> |
|
| 308 |
+<code>filename</code> - the name of the file which the data are to |
|
| 309 |
+be read from. In this example a list of multiple files from a folder is |
|
| 310 |
+used and passed to using <span style=" color: red !important;">purrr</span>.</li> |
|
| 311 |
+<li> |
|
| 312 |
+<code>data_path</code> - The path where the file with the data is |
|
| 313 |
+located</li> |
|
| 314 |
+<li> |
|
| 315 |
+<code>genepix_vars</code> - A list of specific definitions of the |
|
| 316 |
+experiment design. See <span style=" color: red !important;">array_vars()</span> |
|
| 317 |
+</li> |
|
| 318 |
+</ul> |
|
| 319 |
+<p>For this example I use the sub-folder 1 specified using |
|
| 320 |
+<code>genepix_vars$paths[[1]]</code> which is this path under vignette |
|
| 321 |
+folder |
|
| 322 |
+C:/Users/kmwai/AppData/Local/R/win-library/4.2/protGear/extdata/array_data/machine1.</p> |
|
| 323 |
+<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> |
|
| 324 |
+<code class="sourceCode R"><span><span class="co">#### read in all the datasets</span></span> |
|
| 325 |
+<span><span class="co">### list all the file names under data folder</span></span> |
|
| 326 |
+<span><span class="va">filenames</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.files.html" class="external-link">list.files</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/file.path.html" class="external-link">file.path</a></span><span class="op">(</span><span class="va">genepix_vars</span><span class="op">$</span><span class="va">paths</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">)</span>,</span> |
|
| 327 |
+<span> pattern <span class="op">=</span> <span class="st">"*.txt$|*.gpr$"</span>, full.names <span class="op">=</span> <span class="cn">FALSE</span></span> |
|
| 328 |
+<span><span class="op">)</span></span> |
|
| 329 |
+<span><span class="co">#' @___________________read_in_the_files_with_the_text_data_from_the_chip_____________________________</span></span> |
|
| 330 |
+<span><span class="co">### read all the data files and save them in a list</span></span> |
|
| 331 |
+<span><span class="va">data_path</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">genepix_vars</span><span class="op">$</span><span class="va">paths</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span>, <span class="st">"/"</span><span class="op">)</span></span> |
|
| 332 |
+<span><span class="va">data_files</span> <span class="op"><-</span> <span class="fu">purrr</span><span class="fu">::</span><span class="fu"><a href="https://purrr.tidyverse.org/reference/map.html" class="external-link">map</a></span><span class="op">(</span></span> |
|
| 333 |
+<span> .x <span class="op">=</span> <span class="va">filenames</span>,</span> |
|
| 334 |
+<span> .f <span class="op">=</span> <span class="va">read_array_files</span>,</span> |
|
| 335 |
+<span> data_path <span class="op">=</span> <span class="va">data_path</span>,</span> |
|
| 336 |
+<span> genepix_vars <span class="op">=</span> <span class="va">genepix_vars</span></span> |
|
| 337 |
+<span><span class="op">)</span></span> |
|
| 338 |
+<span><span class="va">data_files</span> <span class="op"><-</span> <span class="fu"><a href="https://rlang.r-lib.org/reference/set_names.html" class="external-link">set_names</a></span><span class="op">(</span><span class="va">data_files</span>, <span class="fu">purrr</span><span class="fu">::</span><span class="fu"><a href="https://purrr.tidyverse.org/reference/map.html" class="external-link">map</a></span><span class="op">(</span><span class="va">filenames</span>, <span class="va">name_of_files</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> |
|
| 339 |
+</div> |
|
| 340 |
+</div> |
|
| 341 |
+<div class="section level2"> |
|
| 342 |
+<h2 id="background-correction">Background Correction<a class="anchor" aria-label="anchor" href="#background-correction"></a> |
|
| 343 |
+</h2> |
|
| 344 |
+<p>Background noise is caused by non-specific fluorescence such as |
|
| 345 |
+auto-fluorescence of the glass slide or non-specific binding of |
|
| 346 |
+parameters and reference substances. To cut down the effect of |
|
| 347 |
+background noise we have included different approaches for background |
|
| 348 |
+correction. First, we extract the background values, visualize and |
|
| 349 |
+select the best background approach. We have implemented five different |
|
| 350 |
+approaches;</p> |
|
| 351 |
+<ol style="list-style-type: decimal"> |
|
| 352 |
+<li>Local background subtraction</li> |
|
| 353 |
+<li>Global background subtraction</li> |
|
| 354 |
+<li>Moving minimum background subtraction</li> |
|
| 355 |
+<li>Normal and exponential model (normexp)</li> |
|
| 356 |
+<li>Log-linear background correction (Edwards)</li> |
|
| 357 |
+</ol> |
|
| 358 |
+<p>In ‘<code>.gpr</code>’ files the Background column starts with a |
|
| 359 |
+‘<code>B</code>’ followed by the wavelength or channel. In order to |
|
| 360 |
+perform background correction, we extract the background mean |
|
| 361 |
+fluorescent intensities (MFI’s) using the function <span style=" color: red !important;">extract_bg()</span> . The function |
|
| 362 |
+accepts the arguments <code>iden</code> which is the file identifier, |
|
| 363 |
+<code>data_files</code> a list of data objects with names utilised by |
|
| 364 |
+<code>iden</code> and <code>genepix_vars</code> defined using <span style=" color: red !important;">array_vars()</span> function. We |
|
| 365 |
+utilise the <code>purr::map</code> function to extract the background |
|
| 366 |
+MFI of multiple data files.</p> |
|
| 367 |
+<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r"> |
|
| 368 |
+<code class="sourceCode R"><span><span class="co">## utilising the map package we process a number of files under data_files list</span></span> |
|
| 369 |
+<span><span class="va">dfs</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">data_files</span><span class="op">)</span></span> |
|
| 370 |
+<span><span class="va">allData_bg</span> <span class="op"><-</span> <span class="fu">purrr</span><span class="fu">::</span><span class="fu"><a href="https://purrr.tidyverse.org/reference/map.html" class="external-link">map</a></span><span class="op">(</span>.x <span class="op">=</span> <span class="va">dfs</span>, .f <span class="op">=</span> <span class="va">extract_bg</span>, data_files <span class="op">=</span> <span class="va">data_files</span>, <span class="va">genepix_vars</span><span class="op">)</span></span> |
|
| 371 |
+<span><span class="va">allData_bg</span> <span class="op"><-</span> <span class="fu"><a href="https://rlang.r-lib.org/reference/set_names.html" class="external-link">set_names</a></span><span class="op">(</span><span class="va">allData_bg</span>, <span class="fu">purrr</span><span class="fu">::</span><span class="fu"><a href="https://purrr.tidyverse.org/reference/map.html" class="external-link">map</a></span><span class="op">(</span><span class="va">filenames</span>, <span class="va">name_of_files</span><span class="op">)</span><span class="op">)</span></span> |
|
| 372 |
+<span><span class="va">allData_bg</span> <span class="op"><-</span> <span class="fu">plyr</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/plyr/man/ldply.html" class="external-link">ldply</a></span><span class="op">(</span><span class="va">allData_bg</span><span class="op">)</span></span></code></pre></div> |
|
| 373 |
+<div class="section level3"> |
|
| 374 |
+<h3 id="foreground-vs-background">Foreground vs Background<a class="anchor" aria-label="anchor" href="#foreground-vs-background"></a> |
|
| 375 |
+</h3> |
|
| 376 |
+<p>Before selecting the best background correction approach the MFI |
|
| 377 |
+signals are be inspected visually. In protGear we first utilise the |
|
| 378 |
+function <span style=" color: red !important;">plot_FB()</span> that |
|
| 379 |
+graphs the background, <em>BG_Median</em> and foreground values, |
|
| 380 |
+<em>FBG_Median</em>. On the protGear Shiny platform the visuals are |
|
| 381 |
+interactive and you can identify the features or blocks with strong |
|
| 382 |
+bias.</p> |
|
| 383 |
+<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> |
|
| 384 |
+<code class="sourceCode R"><span><span class="va">p1</span> <span class="op"><-</span> <span class="fu"><a href="../reference/plot_FB.html">plot_FB</a></span><span class="op">(</span><span class="va">allData_bg</span>,</span> |
|
| 385 |
+<span> antigen_name <span class="op">=</span> <span class="st">"antigen"</span>,</span> |
|
| 386 |
+<span> bg_MFI <span class="op">=</span> <span class="st">"BG_Median"</span>, FG_MFI <span class="op">=</span> <span class="st">"FBG_Median"</span>, log <span class="op">=</span> <span class="cn">FALSE</span></span> |
|
| 387 |
+<span><span class="op">)</span></span> |
|
| 388 |
+<span></span> |
|
| 389 |
+<span></span> |
|
| 390 |
+<span><span class="va">p1</span></span></code></pre></div> |
|
| 391 |
+<p><img src="vignette_files/figure-html/bg_vs_fg-1.png" width="700" style="display: block; margin: auto;"></p> |
|
| 392 |
+</div> |
|
| 393 |
+<div class="section level3"> |
|
| 394 |
+<h3 id="background-mfi-by-blocks">Background MFI by blocks<a class="anchor" aria-label="anchor" href="#background-mfi-by-blocks"></a> |
|
| 395 |
+</h3> |
|
| 396 |
+<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r"> |
|
| 397 |
+<code class="sourceCode R"><span><span class="va">p2</span> <span class="op"><-</span> <span class="fu"><a href="../reference/plot_bg.html">plot_bg</a></span><span class="op">(</span></span> |
|
| 398 |
+<span> df <span class="op">=</span> <span class="va">allData_bg</span>, x_axis <span class="op">=</span> <span class="st">"Block"</span>, bg_MFI <span class="op">=</span> <span class="st">"BG_Median"</span>,</span> |
|
| 399 |
+<span> log_mfi <span class="op">=</span> <span class="cn">TRUE</span></span> |
|
| 400 |
+<span><span class="op">)</span></span> |
|
| 401 |
+<span><span class="va">p2</span></span></code></pre></div> |
|
| 402 |
+<p><img src="vignette_files/figure-html/bg_plot-1.png" width="700" style="display: block; margin: auto;"></p> |
|
| 403 |
+</div> |
|
| 404 |
+<div class="section level3"> |
|
| 405 |
+<h3 id="background-correction-1">Background correction<a class="anchor" aria-label="anchor" href="#background-correction-1"></a> |
|
| 406 |
+</h3> |
|
| 407 |
+<p>After background visualization and selecting the best approach the |
|
| 408 |
+array data are merged with their specific sample identifier files.</p> |
|
| 409 |
+<p><em><span style=" color: red !important;">Note:</span></em> Each |
|
| 410 |
+array file must have its own corresponding sample identifier |
|
| 411 |
+<code>.csv</code> file stored in <span style=" color: red !important;">array_vars()</span> function under |
|
| 412 |
+<code>sampleID_path</code>. Check General information section.</p> |
|
| 413 |
+<p>The method of background subtraction selected is specified under |
|
| 414 |
+<span style=" color: red !important;">method</span> below. The |
|
| 415 |
+background correction is performed by <span style=" color: red !important;">bg_correct()</span> function.</p> |
|
| 416 |
+<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r"> |
|
| 417 |
+<code class="sourceCode R"><span><span class="va">sample_ID_merged_dfs</span> <span class="op"><-</span> <span class="fu">purrr</span><span class="fu">::</span><span class="fu"><a href="https://purrr.tidyverse.org/reference/map.html" class="external-link">map</a></span><span class="op">(</span></span> |
|
| 418 |
+<span> .x <span class="op">=</span> <span class="va">dfs</span>, .f <span class="op">=</span> <span class="va">merge_sampleID</span>, data_files <span class="op">=</span> <span class="va">data_files</span>,</span> |
|
| 419 |
+<span> <span class="va">genepix_vars</span>, method <span class="op">=</span> <span class="st">"subtract_local"</span></span> |
|
| 420 |
+<span><span class="op">)</span></span> |
|
| 421 |
+<span><span class="va">sample_ID_merged_dfs</span> <span class="op"><-</span> <span class="fu"><a href="https://rlang.r-lib.org/reference/set_names.html" class="external-link">set_names</a></span><span class="op">(</span><span class="va">sample_ID_merged_dfs</span>, <span class="fu">purrr</span><span class="fu">::</span><span class="fu"><a href="https://purrr.tidyverse.org/reference/map.html" class="external-link">map</a></span><span class="op">(</span><span class="va">filenames</span>, <span class="va">name_of_files</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> |
|
| 422 |
+</div> |
|
| 423 |
+</div> |
|
| 424 |
+<div class="section level2"> |
|
| 425 |
+<h2 id="buffer-spots">Buffer spots<a class="anchor" aria-label="anchor" href="#buffer-spots"></a> |
|
| 426 |
+</h2> |
|
| 427 |
+<p>Buffer spots are specific to the experiment design and are not always |
|
| 428 |
+included. Buffer spots are used to check for unexpected scanning |
|
| 429 |
+artefacts. The buffer spots should have similar values in different |
|
| 430 |
+slides. Some outliers are expected for buffer spots close sample spots |
|
| 431 |
+or landmark. However you can specify the name of your control antigens |
|
| 432 |
+here <span style=" color: blue !important;">buffer_spot="buffer"</span> if you |
|
| 433 |
+do not have buffer spots.</p> |
|
| 434 |
+<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r"> |
|
| 435 |
+<code class="sourceCode R"><span><span class="va">buffer_transp</span> <span class="op"><-</span> <span class="fu">purrr</span><span class="fu">::</span><span class="fu"><a href="https://purrr.tidyverse.org/reference/map.html" class="external-link">map</a></span><span class="op">(</span>.x <span class="op">=</span> <span class="va">sample_ID_merged_dfs</span>, .f <span class="op">=</span> <span class="va">buffer_spots</span>, buffer_spot <span class="op">=</span> <span class="st">"buffer"</span><span class="op">)</span></span> |
|
| 436 |
+<span></span> |
|
| 437 |
+<span><span class="va">buffer_transp</span> <span class="op"><-</span> <span class="fu"><a href="https://rlang.r-lib.org/reference/set_names.html" class="external-link">set_names</a></span><span class="op">(</span><span class="va">buffer_transp</span>, <span class="fu">purrr</span><span class="fu">::</span><span class="fu"><a href="https://purrr.tidyverse.org/reference/map.html" class="external-link">map</a></span><span class="op">(</span><span class="va">filenames</span>, <span class="va">name_of_files</span><span class="op">)</span><span class="op">)</span></span> |
|
| 438 |
+<span></span> |
|
| 439 |
+<span><span class="va">buffers</span> <span class="op"><-</span> <span class="fu">plyr</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/plyr/man/ldply.html" class="external-link">ldply</a></span><span class="op">(</span><span class="va">buffer_transp</span><span class="op">)</span></span> |
|
| 440 |
+<span><span class="fu"><a href="../reference/plot_buffer.html">plot_buffer</a></span><span class="op">(</span><span class="va">buffers</span>, buffer_names <span class="op">=</span> <span class="st">"antigen"</span>, buffer_mfi <span class="op">=</span> <span class="st">"FMedianBG_correct"</span>, slide_id <span class="op">=</span> <span class="st">".id"</span><span class="op">)</span></span></code></pre></div> |
|
| 441 |
+<p><img src="vignette_files/figure-html/buffer_spots_data-1.png" width="700" style="display: block; margin: auto;"></p> |
|
| 442 |
+</div> |
|
| 443 |
+<div class="section level2"> |
|
| 444 |
+<h2 id="coefficient-of-variation-cv">Coefficient of Variation (CV)<a class="anchor" aria-label="anchor" href="#coefficient-of-variation-cv"></a> |
|
| 445 |
+</h2> |
|
| 446 |
+<p>To calculate the CV’s we utilise the <span style=" color: red !important;">cv_estimation()</span> function with |
|
| 447 |
+a <code>cv_cut_off</code> specified , sample identifier variable and |
|
| 448 |
+antigen specified under <code>sampleID_var</code> and |
|
| 449 |
+<code>antigen</code> respectively. The <code>replicate_var</code> and |
|
| 450 |
+<code>mfi_var</code> identifies the variable with the replicate rank |
|
| 451 |
+generated and MFI’s values.</p> |
|
| 452 |
+<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r"> |
|
| 453 |
+<code class="sourceCode R"><span><span class="co">#' @________________________________calculated_cv_for_each_data_file_______________________________________</span></span> |
|
| 454 |
+<span><span class="co">#' data without the selected mean for the best 2 CVs</span></span> |
|
| 455 |
+<span><span class="va">dataCV</span> <span class="op"><-</span> <span class="fu">purrr</span><span class="fu">::</span><span class="fu"><a href="https://purrr.tidyverse.org/reference/map.html" class="external-link">map</a></span><span class="op">(</span></span> |
|
| 456 |
+<span> .x <span class="op">=</span> <span class="va">sample_ID_merged_dfs</span>, .f <span class="op">=</span> <span class="va">cv_estimation</span>, lab_replicates <span class="op">=</span> <span class="fl">3</span>,</span> |
|
| 457 |
+<span> cv_cut_off <span class="op">=</span> <span class="fl">20</span>,</span> |
|
| 458 |
+<span> sampleID_var <span class="op">=</span> <span class="st">"sampleID"</span>, antigen_var <span class="op">=</span> <span class="st">"antigen"</span>, replicate_var <span class="op">=</span> <span class="st">"replicate"</span>,</span> |
|
| 459 |
+<span> mfi_var <span class="op">=</span> <span class="st">"FMedianBG_correct"</span></span> |
|
| 460 |
+<span><span class="op">)</span></span> |
|
| 461 |
+<span></span> |
|
| 462 |
+<span><span class="va">lab_replicates</span> <span class="op"><-</span> <span class="fl">3</span></span> |
|
| 463 |
+<span><span class="va">dataCV</span> <span class="op"><-</span> <span class="fu"><a href="https://rlang.r-lib.org/reference/set_names.html" class="external-link">set_names</a></span><span class="op">(</span><span class="va">dataCV</span>, <span class="fu">purrr</span><span class="fu">::</span><span class="fu"><a href="https://purrr.tidyverse.org/reference/map.html" class="external-link">map</a></span><span class="op">(</span><span class="va">filenames</span>, <span class="va">name_of_files</span><span class="op">)</span><span class="op">)</span></span> |
|
| 464 |
+<span></span> |
|
| 465 |
+<span><span class="va">aa</span> <span class="op"><-</span> <span class="fu">plyr</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/plyr/man/ldply.html" class="external-link">ldply</a></span><span class="op">(</span><span class="va">dataCV</span><span class="op">)</span></span> |
|
| 466 |
+<span><span class="fu">GGally</span><span class="fu">::</span><span class="fu"><a href="https://ggobi.github.io/ggally/reference/ggpairs.html" class="external-link">ggpairs</a></span><span class="op">(</span><span class="va">aa</span>, <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>color <span class="op">=</span> <span class="va">cvCat_all</span><span class="op">)</span>,</span> |
|
| 467 |
+<span> columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="va">lab_replicates</span><span class="op">)</span><span class="op">)</span>, title <span class="op">=</span> <span class="st">""</span>, axisLabels <span class="op">=</span> <span class="st">"show"</span></span> |
|
| 468 |
+<span><span class="op">)</span> <span class="op">+</span></span> |
|
| 469 |
+<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggtheme.html" class="external-link">theme_light</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> |
|
| 470 |
+<p><img src="vignette_files/figure-html/replicates_plot-1.png" width="700" style="display: block; margin: auto;"></p> |
|
| 471 |
+<div class="section level3"> |
|
| 472 |
+<h3 id="summary-of-cv-values">Summary of CV values<a class="anchor" aria-label="anchor" href="#summary-of-cv-values"></a> |
|
| 473 |
+</h3> |
|
| 474 |
+<p>Here we create a summary of the CV values for each sample/slide |
|
| 475 |
+utilising the <span style=" color: red !important;">cv_by_sample_estimation()</span> |
|
| 476 |
+function. This helps to identify samples with high values of CV. On the |
|
| 477 |
+protGear dashboard an interactive table is created to show the summary |
|
| 478 |
+for each sample.</p> |
|
| 479 |
+<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r"> |
|
| 480 |
+<code class="sourceCode R"><span><span class="co">#' @________________________________summary_of_cv_for_each_sample________________________________________</span></span> |
|
| 481 |
+<span><span class="co">#' creates summaries by cv's greater than 20 and less than 20</span></span> |
|
| 482 |
+<span></span> |
|
| 483 |
+<span><span class="va">cv_cut_off</span> <span class="op"><-</span> <span class="fl">20</span></span> |
|
| 484 |
+<span><span class="va">dataCV_sample</span> <span class="op"><-</span> <span class="fu">purrr</span><span class="fu">::</span><span class="fu"><a href="https://purrr.tidyverse.org/reference/map.html" class="external-link">map</a></span><span class="op">(</span></span> |
|
| 485 |
+<span> .x <span class="op">=</span> <span class="va">dataCV</span>, .f <span class="op">=</span> <span class="fu">protGear</span><span class="fu">::</span><span class="va"><a href="../reference/cv_by_sample_estimation.html">cv_by_sample_estimation</a></span>, cv_variable <span class="op">=</span> <span class="st">"cvCat_all"</span>,</span> |
|
| 486 |
+<span> lab_replicates <span class="op">=</span> <span class="fl">3</span></span> |
|
| 487 |
+<span><span class="op">)</span></span> |
|
| 488 |
+<span><span class="va">dataCV_sample</span> <span class="op"><-</span> <span class="fu"><a href="https://rlang.r-lib.org/reference/set_names.html" class="external-link">set_names</a></span><span class="op">(</span><span class="va">dataCV_sample</span>, <span class="fu">purrr</span><span class="fu">::</span><span class="fu"><a href="https://purrr.tidyverse.org/reference/map.html" class="external-link">map</a></span><span class="op">(</span><span class="va">filenames</span>, <span class="va">name_of_files</span><span class="op">)</span><span class="op">)</span></span> |
|
| 489 |
+<span><span class="va">all_cv_sample</span> <span class="op"><-</span> <span class="fu">plyr</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/plyr/man/ldply.html" class="external-link">ldply</a></span><span class="op">(</span><span class="va">dataCV_sample</span><span class="op">)</span></span></code></pre></div> |
|
| 490 |
+<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> |
|
| 491 |
+<code class="sourceCode R"><span><span class="va">less_20</span> <span class="op"><-</span> <span class="fu">rlang</span><span class="fu">::</span><span class="fu"><a href="https://rlang.r-lib.org/reference/sym.html" class="external-link">sym</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"CV <= "</span>, <span class="va">cv_cut_off</span>, <span class="st">"_perc"</span><span class="op">)</span><span class="op">)</span></span> |
|
| 492 |
+<span><span class="va">gt_20</span> <span class="op"><-</span> <span class="fu">rlang</span><span class="fu">::</span><span class="fu"><a href="https://rlang.r-lib.org/reference/sym.html" class="external-link">sym</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"CV > "</span>, <span class="va">cv_cut_off</span>, <span class="st">"_perc"</span><span class="op">)</span><span class="op">)</span></span> |
|
| 493 |
+<span></span> |
|
| 494 |
+<span><span class="va">less_20_per</span> <span class="op"><-</span> <span class="fu">rlang</span><span class="fu">::</span><span class="fu"><a href="https://rlang.r-lib.org/reference/sym.html" class="external-link">sym</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"% CV <="</span>, <span class="va">cv_cut_off</span><span class="op">)</span><span class="op">)</span></span> |
|
| 495 |
+<span><span class="va">gt_20_per</span> <span class="op"><-</span> <span class="fu">rlang</span><span class="fu">::</span><span class="fu"><a href="https://rlang.r-lib.org/reference/sym.html" class="external-link">sym</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"% CV >"</span>, <span class="va">cv_cut_off</span><span class="op">)</span><span class="op">)</span></span> |
|
| 496 |
+<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="va">all_cv_sample</span><span class="op">)</span> <span class="op">+</span></span> |
|
| 497 |
+<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_violin.html" class="external-link">geom_violin</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span><span class="va">.id</span>, <span class="va">`CV <= 20_perc`</span>, color <span class="op">=</span> <span class="st">"% CV =<20"</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span> |
|
| 498 |
+<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_violin.html" class="external-link">geom_violin</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span><span class="va">.id</span>, <span class="va">`CV > 20_perc`</span>, color <span class="op">=</span> <span class="st">"% CV >20"</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span> |
|
| 499 |
+<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_violin.html" class="external-link">geom_violin</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span><span class="va">.id</span>, <span class="va">Others_perc</span>, color <span class="op">=</span> <span class="st">"Others"</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span> |
|
| 500 |
+<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">ylab</a></span><span class="op">(</span><span class="st">"% of CV"</span><span class="op">)</span> <span class="op">+</span></span> |
|
| 501 |
+<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggtheme.html" class="external-link">theme_minimal</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span> |
|
| 502 |
+<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">ggtitle</a></span><span class="op">(</span><span class="st">"% of CV >20 or <=20 for each slide all repeats considered"</span><span class="op">)</span></span></code></pre></div> |
|
| 503 |
+<p><img src="vignette_files/figure-html/cv_by_sample-1.png" width="700" style="display: block; margin: auto;"></p> |
|
| 504 |
+</div> |
|
| 505 |
+<div class="section level3"> |
|
| 506 |
+<h3 id="best-replicates">Best replicates<a class="anchor" aria-label="anchor" href="#best-replicates"></a> |
|
| 507 |
+</h3> |
|
| 508 |
+<p>We have implemented a function <span style=" color: red !important;">best_CV_estimation()</span> to |
|
| 509 |
+select the best replicates if an experiment has more than 2 technical |
|
| 510 |
+replicates. This helps to select the less variable replicates.</p> |
|
| 511 |
+<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r"> |
|
| 512 |
+<code class="sourceCode R"><span><span class="co">#' @________________________________data_with_selected_best_2_CV_______________________________________</span></span> |
|
| 513 |
+<span><span class="co">#' data with the selected mean for the best 2 CVs</span></span> |
|
| 514 |
+<span><span class="va">dataCV_best2</span> <span class="op"><-</span> <span class="fu">purrr</span><span class="fu">::</span><span class="fu"><a href="https://purrr.tidyverse.org/reference/map.html" class="external-link">map</a></span><span class="op">(</span></span> |
|
| 515 |
+<span> .x <span class="op">=</span> <span class="va">dataCV</span>, .f <span class="op">=</span> <span class="va">best_CV_estimation</span>, slide_id <span class="op">=</span> <span class="st">"iden"</span>, lab_replicates <span class="op">=</span> <span class="fl">3</span>,</span> |
|
| 516 |
+<span> cv_cut_off <span class="op">=</span> <span class="fl">20</span></span> |
|
| 517 |
+<span><span class="op">)</span></span> |
|
| 518 |
+<span></span> |
|
| 519 |
+<span><span class="co">## give the names to the returned list</span></span> |
|
| 520 |
+<span><span class="va">dataCV_best2</span> <span class="op"><-</span> <span class="fu"><a href="https://rlang.r-lib.org/reference/set_names.html" class="external-link">set_names</a></span><span class="op">(</span><span class="va">dataCV_best2</span>, <span class="fu">purrr</span><span class="fu">::</span><span class="fu"><a href="https://purrr.tidyverse.org/reference/map.html" class="external-link">map</a></span><span class="op">(</span><span class="va">filenames</span>, <span class="va">name_of_files</span><span class="op">)</span><span class="op">)</span></span> |
|
| 521 |
+<span></span> |
|
| 522 |
+<span></span> |
|
| 523 |
+<span><span class="va">dataCV_sample_best2</span> <span class="op"><-</span> <span class="fu">purrr</span><span class="fu">::</span><span class="fu"><a href="https://purrr.tidyverse.org/reference/map.html" class="external-link">map</a></span><span class="op">(</span></span> |
|
| 524 |
+<span> .x <span class="op">=</span> <span class="va">dataCV_best2</span>, .f <span class="op">=</span> <span class="va">cv_by_sample_estimation</span>,</span> |
|
| 525 |
+<span> cv_variable <span class="op">=</span> <span class="st">"best_CV_cat"</span>, lab_replicates <span class="op">=</span> <span class="fl">3</span></span> |
|
| 526 |
+<span><span class="op">)</span></span> |
|
| 527 |
+<span><span class="va">dataCV_sample_best2</span> <span class="op"><-</span> <span class="fu"><a href="https://rlang.r-lib.org/reference/set_names.html" class="external-link">set_names</a></span><span class="op">(</span><span class="va">dataCV_sample_best2</span>, <span class="fu">purrr</span><span class="fu">::</span><span class="fu"><a href="https://purrr.tidyverse.org/reference/map.html" class="external-link">map</a></span><span class="op">(</span><span class="va">filenames</span>, <span class="va">name_of_files</span><span class="op">)</span><span class="op">)</span></span> |
|
| 528 |
+<span><span class="va">all_cv_sample_best2</span> <span class="op"><-</span> <span class="fu">plyr</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/plyr/man/ldply.html" class="external-link">ldply</a></span><span class="op">(</span><span class="va">dataCV_sample_best2</span><span class="op">)</span></span></code></pre></div> |
|
| 529 |
+<p>On the violin below we observe that with selecting the less variable |
|
| 530 |
+replicates , the percentage of the “good CV” values increases.</p> |
|
| 531 |
+<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r"> |
|
| 532 |
+<code class="sourceCode R"><span><span class="co">## plot only the CV perccentages</span></span> |
|
| 533 |
+<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="va">all_cv_sample_best2</span><span class="op">)</span> <span class="op">+</span></span> |
|
| 534 |
+<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_violin.html" class="external-link">geom_violin</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span><span class="va">.id</span>, <span class="va">`CV <= 20_perc`</span>, color <span class="op">=</span> <span class="st">"% CV =<20"</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span> |
|
| 535 |
+<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_violin.html" class="external-link">geom_violin</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span><span class="va">.id</span>, <span class="va">`CV > 20_perc`</span>, color <span class="op">=</span> <span class="st">"% CV >20"</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span> |
|
| 536 |
+<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_violin.html" class="external-link">geom_violin</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span><span class="va">.id</span>, <span class="va">Others_perc</span>, color <span class="op">=</span> <span class="st">"Others"</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span> |
|
| 537 |
+<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">ylab</a></span><span class="op">(</span><span class="st">"% of CV"</span><span class="op">)</span> <span class="op">+</span></span> |
|
| 538 |
+<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggtheme.html" class="external-link">theme_minimal</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span> |
|
| 539 |
+<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">ggtitle</a></span><span class="op">(</span><span class="st">"% of CV >20 or <=20 for each slide"</span><span class="op">)</span></span></code></pre></div> |
|
| 540 |
+<p><img src="vignette_files/figure-html/best_cv_plot-1.png" width="700" style="display: block; margin: auto;"></p> |
|
| 541 |
+</div> |
|
| 542 |
+</div> |
|
| 543 |
+<div class="section level2"> |
|
| 544 |
+<h2 id="tag-subtraction">Tag subtraction<a class="anchor" aria-label="anchor" href="#tag-subtraction"></a> |
|
| 545 |
+</h2> |
|
| 546 |
+<p>Tag subtraction is applied for antigens containing purification tags. |
|
| 547 |
+A file with the specific TAG name for each antigen is loaded. The file |
|
| 548 |
+has the <code>antigen,TAG and TAG_name</code> and the TAG_name must be |
|
| 549 |
+part of the antigens listed.</p> |
|
| 550 |
+<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> |
|
| 551 |
+<code class="sourceCode R"><span><span class="va">tag_file</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/utils/read.table.html" class="external-link">read.csv</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata/TAG_antigens.csv"</span>, package <span class="op">=</span> <span class="st">"protGear"</span><span class="op">)</span><span class="op">)</span></span> |
|
| 552 |
+<span><span class="va">tag_antigens</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"CD4TAG"</span>, <span class="st">"GST"</span>, <span class="st">"MBP"</span><span class="op">)</span></span> |
|
| 553 |
+<span><span class="va">batch_vars</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>machine <span class="op">=</span> <span class="st">"m1"</span>, day <span class="op">=</span> <span class="st">"0520"</span><span class="op">)</span></span></code></pre></div> |
|
| 554 |
+<div class="section level3"> |
|
| 555 |
+<h3 id="overview-of-the-tag-file">Overview of the TAG file<a class="anchor" aria-label="anchor" href="#overview-of-the-tag-file"></a> |
|
| 556 |
+</h3> |
|
| 557 |
+<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r"> |
|
| 558 |
+<code class="sourceCode R"><span><span class="va">tb1</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">tag_file</span>, n <span class="op">=</span> <span class="fl">10</span><span class="op">)</span><span class="op">)</span></span> |
|
| 559 |
+<span><span class="va">tb1</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span> |
|
| 560 |
+<span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span> |
|
| 561 |
+<span> <span class="fu"><a href="https://rdrr.io/pkg/kableExtra/man/kable_styling.html" class="external-link">kable_styling</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> |
|
| 562 |
+<table class="table table" style="margin-left: auto; margin-right: auto;"> |
|
| 563 |
+<thead><tr> |
|
| 564 |
+<th style="text-align:left;"> |
|
| 565 |
+antigen |
|
| 566 |
+</th> |
|
| 567 |
+<th style="text-align:right;"> |
|
| 568 |
+TAG |
|
| 569 |
+</th> |
|
| 570 |
+<th style="text-align:left;"> |
|
| 571 |
+TAG_name |
|
| 572 |
+</th> |
|
| 573 |
+</tr></thead> |
|
| 574 |
+<tbody> |
|
| 575 |
+<tr> |
|
| 576 |
+<td style="text-align:left;"> |
|
| 577 |
+AARP |
|
| 578 |
+</td> |
|
| 579 |
+<td style="text-align:right;"> |
|
| 580 |
+0 |
|
| 581 |
+</td> |
|
| 582 |
+<td style="text-align:left;"> |
|
| 583 |
+CD4TAG |
|
| 584 |
+</td> |
|
| 585 |
+</tr> |
|
| 586 |
+<tr> |
|
| 587 |
+<td style="text-align:left;"> |
|
| 588 |
+AMA1 |
|
| 589 |
+</td> |
|
| 590 |
+<td style="text-align:right;"> |
|
| 591 |
+0 |
|
| 592 |
+</td> |
|
| 593 |
+<td style="text-align:left;"> |
|
| 594 |
+CD4TAG |
|
| 595 |
+</td> |
|
| 596 |
+</tr> |
|
| 597 |
+<tr> |
|
| 598 |
+<td style="text-align:left;"> |
|
| 599 |
+ASP |
|
| 600 |
+</td> |
|
| 601 |
+<td style="text-align:right;"> |
|
| 602 |
+0 |
|
| 603 |
+</td> |
|
| 604 |
+<td style="text-align:left;"> |
|
| 605 |
+CD4TAG |
|
| 606 |
+</td> |
|
| 607 |
+</tr> |
|
| 608 |
+<tr> |
|
| 609 |
+<td style="text-align:left;"> |
|
| 610 |
+CD4TAG |
|
| 611 |
+</td> |
|
| 612 |
+<td style="text-align:right;"> |
|
| 613 |
+99 |
|
| 614 |
+</td> |
|
| 615 |
+<td style="text-align:left;"> |
|
| 616 |
+NO_TAG |
|
| 617 |
+</td> |
|
| 618 |
+</tr> |
|
| 619 |
+<tr> |
|
| 620 |
+<td style="text-align:left;"> |
|
| 621 |
+CLAG3.2 |
|
| 622 |
+</td> |
|
| 623 |
+<td style="text-align:right;"> |
|
| 624 |
+0 |
|
| 625 |
+</td> |
|
| 626 |
+<td style="text-align:left;"> |
|
| 627 |
+CD4TAG |
|
| 628 |
+</td> |
|
| 629 |
+</tr> |
|
| 630 |
+<tr> |
|
| 631 |
+<td style="text-align:left;"> |
|
| 632 |
+EBA140 |
|
| 633 |
+</td> |
|
| 634 |
+<td style="text-align:right;"> |
|
| 635 |
+0 |
|
| 636 |
+</td> |
|
| 637 |
+<td style="text-align:left;"> |
|
| 638 |
+CD4TAG |
|
| 639 |
+</td> |
|
| 640 |
+</tr> |
|
| 641 |
+<tr> |
|
| 642 |
+<td style="text-align:left;"> |
|
| 643 |
+EBA175 |
|
| 644 |
+</td> |
|
| 645 |
+<td style="text-align:right;"> |
|
| 646 |
+0 |
|
| 647 |
+</td> |
|
| 648 |
+<td style="text-align:left;"> |
|
| 649 |
+CD4TAG |
|
| 650 |
+</td> |
|
| 651 |
+</tr> |
|
| 652 |
+<tr> |
|
| 653 |
+<td style="text-align:left;"> |
|
| 654 |
+EBA181 |
|
| 655 |
+</td> |
|
| 656 |
+<td style="text-align:right;"> |
|
| 657 |
+0 |
|
| 658 |
+</td> |
|
| 659 |
+<td style="text-align:left;"> |
|
| 660 |
+CD4TAG |
|
| 661 |
+</td> |
|
| 662 |
+</tr> |
|
| 663 |
+<tr> |
|
| 664 |
+<td style="text-align:left;"> |
|
| 665 |
+ETRAMP10.2 |
|
| 666 |
+</td> |
|
| 667 |
+<td style="text-align:right;"> |
|
| 668 |
+0 |
|
| 669 |
+</td> |
|
| 670 |
+<td style="text-align:left;"> |
|
| 671 |
+CD4TAG |
|
| 672 |
+</td> |
|
| 673 |
+</tr> |
|
| 674 |
+<tr> |
|
| 675 |
+<td style="text-align:left;"> |
|
| 676 |
+GAMA |
|
| 677 |
+</td> |
|
| 678 |
+<td style="text-align:right;"> |
|
| 679 |
+0 |
|
| 680 |
+</td> |
|
| 681 |
+<td style="text-align:left;"> |
|
| 682 |
+CD4TAG |
|
| 683 |
+</td> |
|
| 684 |
+</tr> |
|
| 685 |
+</tbody> |
|
| 686 |
+</table> |
|
| 687 |
+</div> |
|
| 688 |
+<div class="section level3"> |
|
| 689 |
+<h3 id="subtracting-the-tag-values">Subtracting the TAG values<a class="anchor" aria-label="anchor" href="#subtracting-the-tag-values"></a> |
|
| 690 |
+</h3> |
|
| 691 |
+<p>The function <span style=" color: red !important;">tag_subtract()</span> implements the |
|
| 692 |
+TAG subtration by matching the TAG names with the corresponding TAG |
|
| 693 |
+values.</p> |
|
| 694 |
+<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r"> |
|
| 695 |
+<code class="sourceCode R"><span><span class="co">#' @________________________________subtract_the_tag_values_______________________________________</span></span> |
|
| 696 |
+<span><span class="co">#'</span></span> |
|
| 697 |
+<span><span class="co">## tag subtract</span></span> |
|
| 698 |
+<span><span class="co">## read in the KILCHip TAG file to substract GST-1, MBP -2 and CD4TAG - 0 file</span></span> |
|
| 699 |
+<span><span class="va">dataCV_tag</span> <span class="op"><-</span> <span class="fu">purrr</span><span class="fu">::</span><span class="fu"><a href="https://purrr.tidyverse.org/reference/map.html" class="external-link">map</a></span><span class="op">(</span></span> |
|
| 700 |
+<span> .x <span class="op">=</span> <span class="va">dataCV_best2</span>, .f <span class="op">=</span> <span class="va">tag_subtract</span>,</span> |
|
| 701 |
+<span> tag_antigens <span class="op">=</span> <span class="va">tag_antigens</span>, mean_best_CV_var <span class="op">=</span> <span class="st">"mean_best_CV"</span>, tag_file <span class="op">=</span> <span class="va">tag_file</span>,</span> |
|
| 702 |
+<span> antigen_var <span class="op">=</span> <span class="st">"antigen"</span>,</span> |
|
| 703 |
+<span> batch_vars <span class="op">=</span> <span class="va">batch_vars</span></span> |
|
| 704 |
+<span><span class="op">)</span></span> |
|
| 705 |
+<span><span class="va">dataCV_tag</span> <span class="op"><-</span> <span class="fu"><a href="https://rlang.r-lib.org/reference/set_names.html" class="external-link">set_names</a></span><span class="op">(</span><span class="va">dataCV_tag</span>, <span class="fu">purrr</span><span class="fu">::</span><span class="fu"><a href="https://purrr.tidyverse.org/reference/map.html" class="external-link">map</a></span><span class="op">(</span><span class="va">filenames</span>, <span class="va">name_of_files</span><span class="op">)</span><span class="op">)</span></span> |
|
| 706 |
+<span><span class="va">dataCV_tag</span> <span class="op"><-</span> <span class="fu">plyr</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/plyr/man/ldply.html" class="external-link">ldply</a></span><span class="op">(</span><span class="va">dataCV_tag</span><span class="op">)</span></span></code></pre></div> |
|
| 707 |
+<p>In this example here we plot a graph of antigens Tagged with GST |
|
| 708 |
+before and after TAG subtraction.</p> |
|
| 709 |
+<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> |
|
| 710 |
+<code class="sourceCode R"><span><span class="va">aaa</span> <span class="op"><-</span> <span class="va">dataCV_tag</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span> |
|
| 711 |
+<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">TAG_name</span> <span class="op">==</span> <span class="st">"GST"</span><span class="op">)</span></span> |
|
| 712 |
+<span></span> |
|
| 713 |
+<span><span class="va">aaa</span> <span class="op"><-</span> <span class="va">aaa</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span> |
|
| 714 |
+<span> <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">.id</span>, <span class="va">sampleID</span>, <span class="va">antigen</span>, <span class="va">mean_best_CV</span>, <span class="va">mean_best_CV_tag</span><span class="op">)</span></span> |
|
| 715 |
+<span></span> |
|
| 716 |
+<span><span class="va">aaa</span> <span class="op"><-</span> <span class="va">aaa</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span> |
|
| 717 |
+<span> <span class="fu"><a href="https://tidyr.tidyverse.org/reference/gather.html" class="external-link">gather</a></span><span class="op">(</span><span class="va">measure</span>, <span class="va">mfi</span>, <span class="op">-</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">.id</span><span class="op">:</span><span class="va">antigen</span><span class="op">)</span><span class="op">)</span></span> |
|
| 718 |
+<span></span> |
|
| 719 |
+<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="va">aaa</span>, <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">as.factor</a></span><span class="op">(</span><span class="va">antigen</span><span class="op">)</span>, <span class="va">mfi</span>, color <span class="op">=</span> <span class="va">measure</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span> |
|
| 720 |
+<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_boxplot.html" class="external-link">geom_boxplot</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>fill <span class="op">=</span> <span class="va">measure</span><span class="op">)</span>, alpha <span class="op">=</span> <span class="fl">0.5</span><span class="op">)</span> <span class="op">+</span></span> |
|
| 721 |
+<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggtheme.html" class="external-link">theme_light</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span> |
|
| 722 |
+<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">xlab</a></span><span class="op">(</span><span class="st">"antigen name"</span><span class="op">)</span> <span class="op">+</span></span> |
|
| 723 |
+<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">ggtitle</a></span><span class="op">(</span><span class="st">"Before and after TAG subtraction"</span><span class="op">)</span> <span class="op">+</span></span> |
|
| 724 |
+<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/theme.html" class="external-link">theme</a></span><span class="op">(</span>axis.text.x <span class="op">=</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/element.html" class="external-link">element_text</a></span><span class="op">(</span>angle <span class="op">=</span> <span class="fl">45</span>, hjust <span class="op">=</span> <span class="fl">1</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> |
|
| 725 |
+<p><img src="vignette_files/figure-html/before_after_tag-1.png" width="700" style="display: block; margin: auto;"></p> |
|
| 726 |
+</div> |
|
| 727 |
+</div> |
|
| 728 |
+<div class="section level2"> |
|
| 729 |
+<h2 id="normalisation">Normalisation<a class="anchor" aria-label="anchor" href="#normalisation"></a> |
|
| 730 |
+</h2> |
|
| 731 |
+<p>To normalise the data, we create a matrix <code>matrix_antigen</code> |
|
| 732 |
+with all the data combined. We ensure the slide identifier is included |
|
| 733 |
+as row names of the matrix or we have a way to join them after |
|
| 734 |
+normalisation. The <code>array_matrix</code> matrix is used to hold |
|
| 735 |
+these parameters. In place of <code>AMA1</code> in the example below you |
|
| 736 |
+use one of your features or antigen. We have implemented four different |
|
| 737 |
+normalisation techniques;</p> |
|
| 738 |
+<ol style="list-style-type: decimal"> |
|
| 739 |
+<li> |
|
| 740 |
+<span class="math inline">\(Log_2\)</span> normalisation</li> |
|
| 741 |
+<li>Loess normalisation</li> |
|
| 742 |
+<li>RLM normalisation</li> |
|
| 743 |
+<li>VSN normalisation.</li> |
|
| 744 |
+</ol> |
|
| 745 |
+<div class="sourceCode" id="cb24"><pre class="downlit sourceCode r"> |
|
| 746 |
+<code class="sourceCode R"><span><span class="va">df_to_normalise</span> <span class="op"><-</span> <span class="va">dataCV_tag</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span> |
|
| 747 |
+<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">ungroup</a></span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span> |
|
| 748 |
+<span> <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span>slide <span class="op">=</span> <span class="va">.id</span>, <span class="va">sampleID</span>, <span class="va">sample_array_ID</span>, <span class="va">antigen</span>, <span class="va">mean_best_CV</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span> |
|
| 749 |
+<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">sampleID</span>, <span class="va">slide</span><span class="op">)</span></span> |
|
| 750 |
+<span><span class="va">df_to_normalise</span><span class="op">$</span><span class="va">sample_index</span> <span class="op"><-</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_data.html" class="external-link">group_indices</a></span><span class="op">(</span>.data <span class="op">=</span> <span class="va">df_to_normalise</span><span class="op">)</span></span> |
|
| 751 |
+<span></span> |
|
| 752 |
+<span><span class="co">###</span></span> |
|
| 753 |
+<span><span class="va">to_normalise</span> <span class="op"><-</span> <span class="va">df_to_normalise</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span> |
|
| 754 |
+<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">ungroup</a></span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span> |
|
| 755 |
+<span> <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">slide</span>, <span class="op">-</span><span class="va">sampleID</span>, <span class="op">-</span><span class="va">sample_array_ID</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span> |
|
| 756 |
+<span> <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">antigen</span>, <span class="va">sample_index</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/everything.html" class="external-link">everything</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span> |
|
| 757 |
+<span> <span class="fu"><a href="https://tidyr.tidyverse.org/reference/gather.html" class="external-link">gather</a></span><span class="op">(</span><span class="va">variable</span>, <span class="va">value</span>, <span class="op">-</span><span class="op">(</span><span class="va">antigen</span><span class="op">:</span><span class="va">sample_index</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span> |
|
| 758 |
+<span> <span class="fu"><a href="https://tidyr.tidyverse.org/reference/unite.html" class="external-link">unite</a></span><span class="op">(</span><span class="va">temp</span>, <span class="va">antigen</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span> |
|
| 759 |
+<span> <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">variable</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span> |
|
| 760 |
+<span> <span class="fu"><a href="https://tidyr.tidyverse.org/reference/spread.html" class="external-link">spread</a></span><span class="op">(</span><span class="va">temp</span>, <span class="va">value</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span> |
|
| 761 |
+<span> <span class="fu"><a href="https://rdrr.io/r/base/as.data.frame.html" class="external-link">as.data.frame</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span></span> |
|
| 762 |
+<span></span> |
|
| 763 |
+<span><span class="co">### get the row names of the machine data</span></span> |
|
| 764 |
+<span><span class="fu"><a href="https://rdrr.io/r/base/row.names.html" class="external-link">row.names</a></span><span class="op">(</span><span class="va">to_normalise</span><span class="op">)</span> <span class="op"><-</span> <span class="va">to_normalise</span><span class="op">$</span><span class="va">sample_index</span></span> |
|
| 765 |
+<span><span class="co"># batch_all <- as.factor(paste0(to_normalise$machine,"/",to_normalise$day))</span></span> |
|
| 766 |
+<span><span class="co"># machines <- as.factor(to_normalise$machine)</span></span> |
|
| 767 |
+<span><span class="co"># day_batches <- as.factor(to_normalise$day)</span></span> |
|
| 768 |
+<span></span> |
|
| 769 |
+<span><span class="co">## create the matrix to normalise</span></span> |
|
| 770 |
+<span><span class="va">matrix_antigen</span> <span class="op"><-</span> <span class="va">to_normalise</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span> |
|
| 771 |
+<span> <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">sample_index</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span> |
|
| 772 |
+<span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">as.matrix</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span></span> |
|
| 773 |
+<span></span> |
|
| 774 |
+<span></span> |
|
| 775 |
+<span><span class="co">## create the matrix to hold the important parameters</span></span> |
|
| 776 |
+<span><span class="co">## in place of AMA1 you use one of your features or antigen</span></span> |
|
| 777 |
+<span><span class="va">array_matrix</span> <span class="op"><-</span> <span class="va">df_to_normalise</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span> |
|
| 778 |
+<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">antigen</span> <span class="op">==</span> <span class="st">"AMA1"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span> |
|
| 779 |
+<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">ungroup</a></span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span> |
|
| 780 |
+<span> <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">sample_array_ID</span>, <span class="va">sample_index</span>, <span class="va">slide</span><span class="op">)</span></span> |
|
| 781 |
+<span></span> |
|
| 782 |
+<span><span class="va">control_antigens</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"CommercialHumanIgG"</span>, <span class="st">"CD4TAG"</span><span class="op">)</span></span></code></pre></div> |
|
| 783 |
+<p>The <span style=" color: red !important;">matrix_normalise()</span> function |
|
| 784 |
+is used to normalise the data and returns a list of plots and a matrix |
|
| 785 |
+of normalised values. A plot is returned if |
|
| 786 |
+<code>return_plot = TRUE</code> otherwise only a matrix of normalised |
|
| 787 |
+values will be returned.</p> |
|
| 788 |
+<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r"> |
|
| 789 |
+<code class="sourceCode R"><span><span class="va">normlise_df</span> <span class="op"><-</span> <span class="fu"><a href="../reference/matrix_normalise.html">matrix_normalise</a></span><span class="op">(</span><span class="va">matrix_antigen</span>,</span> |
|
| 790 |
+<span> method <span class="op">=</span> <span class="st">"vsn"</span>, array_matrix <span class="op">=</span> <span class="va">array_matrix</span>,</span> |
|
| 791 |
+<span> return_plot <span class="op">=</span> <span class="cn">TRUE</span>, control_antigens <span class="op">=</span> <span class="va">control_antigens</span></span> |
|
| 792 |
+<span><span class="op">)</span></span> |
|
| 793 |
+<span></span> |
|
| 794 |
+<span><span class="va">normlise_df</span><span class="op">$</span><span class="va">plot_normalisation</span></span></code></pre></div> |
|
| 795 |
+<p><img src="vignette_files/figure-html/normalised_df-1.png" width="700" style="display: block; margin: auto;"></p> |
|
| 796 |
+<div class="section level3"> |
|
| 797 |
+<h3 id="compare-normalisation-methods">Compare normalisation methods<a class="anchor" aria-label="anchor" href="#compare-normalisation-methods"></a> |
|
| 798 |
+</h3> |
|
| 799 |
+<p>On the dashboard we compare the different normalisation techniques |
|
| 800 |
+using the <span style=" color: red !important;">mutiple_plot()</span> function after |
|
| 801 |
+loading the data.</p> |
|
| 802 |
+<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r"> |
|
| 803 |
+<code class="sourceCode R"><span><span class="va">control_antigens</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"CommercialHumanIgG"</span>, <span class="st">"CD4TAG"</span><span class="op">)</span></span> |
|
| 804 |
+<span><span class="co">## no normalisation</span></span> |
|
| 805 |
+<span><span class="va">normalise_list_none</span> <span class="op"><-</span> <span class="fu"><a href="../reference/matrix_normalise.html">matrix_normalise</a></span><span class="op">(</span></span> |
|
| 806 |
+<span> matrix_antigen <span class="op">=</span> <span class="va">matrix_antigen</span>,</span> |
|
| 807 |
+<span> method <span class="op">=</span> <span class="st">"none"</span>,</span> |
|
| 808 |
+<span> array_matrix <span class="op">=</span> <span class="va">array_matrix</span>,</span> |
|
| 809 |
+<span> return_plot <span class="op">=</span> <span class="cn">TRUE</span>,</span> |
|
| 810 |
+<span> control_antigens <span class="op">=</span> <span class="va">control_antigens</span></span> |
|
| 811 |
+<span><span class="op">)</span></span> |
|
| 812 |
+<span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">normalise_list_none</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"matrix_antigen_none"</span>, <span class="st">"plot_none"</span><span class="op">)</span></span> |
|
| 813 |
+<span><span class="co">## log2 normalisation</span></span> |
|
| 814 |
+<span><span class="va">normalise_list_log</span> <span class="op"><-</span> <span class="fu"><a href="../reference/matrix_normalise.html">matrix_normalise</a></span><span class="op">(</span></span> |
|
| 815 |
+<span> matrix_antigen <span class="op">=</span> <span class="va">matrix_antigen</span>,</span> |
|
| 816 |
+<span> method <span class="op">=</span> <span class="st">"log2"</span>,</span> |
|
| 817 |
+<span> array_matrix <span class="op">=</span> <span class="va">array_matrix</span>,</span> |
|
| 818 |
+<span> return_plot <span class="op">=</span> <span class="cn">TRUE</span>,</span> |
|
| 819 |
+<span> control_antigens <span class="op">=</span> <span class="va">control_antigens</span></span> |
|
| 820 |
+<span><span class="op">)</span></span> |
|
| 821 |
+<span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">normalise_list_log</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"matrix_antigen_log"</span>, <span class="st">"plot_log"</span><span class="op">)</span></span> |
|
| 822 |
+<span><span class="co">## vsn normalisation</span></span> |
|
| 823 |
+<span><span class="va">normalise_list_vsn</span> <span class="op"><-</span> <span class="fu"><a href="../reference/matrix_normalise.html">matrix_normalise</a></span><span class="op">(</span></span> |
|
| 824 |
+<span> matrix_antigen <span class="op">=</span> <span class="va">matrix_antigen</span>,</span> |
|
| 825 |
+<span> method <span class="op">=</span> <span class="st">"vsn"</span>,</span> |
|
| 826 |
+<span> array_matrix <span class="op">=</span> <span class="va">array_matrix</span>,</span> |
|
| 827 |
+<span> return_plot <span class="op">=</span> <span class="cn">TRUE</span>,</span> |
|
| 828 |
+<span> control_antigens <span class="op">=</span> <span class="va">control_antigens</span></span> |
|
| 829 |
+<span><span class="op">)</span></span> |
|
| 830 |
+<span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">normalise_list_vsn</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"matrix_antigen_vsn"</span>, <span class="st">"plot_vsn"</span><span class="op">)</span></span> |
|
| 831 |
+<span><span class="co">## cyclic loess with log</span></span> |
|
| 832 |
+<span><span class="va">normalise_list_cyclic_loess_log</span> <span class="op"><-</span> <span class="fu"><a href="../reference/matrix_normalise.html">matrix_normalise</a></span><span class="op">(</span></span> |
|
| 833 |
+<span> matrix_antigen <span class="op">=</span> <span class="va">matrix_antigen</span>,</span> |
|
| 834 |
+<span> method <span class="op">=</span> <span class="st">"cyclic_loess_log"</span>,</span> |
|
| 835 |
+<span> array_matrix <span class="op">=</span> <span class="va">array_matrix</span>,</span> |
|
| 836 |
+<span> return_plot <span class="op">=</span> <span class="cn">TRUE</span>,</span> |
|
| 837 |
+<span> control_antigens <span class="op">=</span> <span class="va">control_antigens</span></span> |
|
| 838 |
+<span><span class="op">)</span></span> |
|
| 839 |
+<span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">normalise_list_cyclic_loess_log</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span> |
|
| 840 |
+<span> <span class="st">"matrix_antigen_cyclic_loess_log"</span>,</span> |
|
| 841 |
+<span> <span class="st">"plot_cyclic_loess_log"</span></span> |
|
| 842 |
+<span><span class="op">)</span></span> |
|
| 843 |
+<span></span> |
|
| 844 |
+<span></span> |
|
| 845 |
+<span><span class="va">normalise_list_rlm</span> <span class="op"><-</span> <span class="fu"><a href="../reference/matrix_normalise.html">matrix_normalise</a></span><span class="op">(</span></span> |
|
| 846 |
+<span> matrix_antigen <span class="op">=</span> <span class="va">matrix_antigen</span>,</span> |
|
| 847 |
+<span> method <span class="op">=</span> <span class="st">"rlm"</span>,</span> |
|
| 848 |
+<span> array_matrix <span class="op">=</span> <span class="va">array_matrix</span>,</span> |
|
| 849 |
+<span> return_plot <span class="op">=</span> <span class="cn">TRUE</span>,</span> |
|
| 850 |
+<span> control_antigens <span class="op">=</span> <span class="va">control_antigens</span></span> |
|
| 851 |
+<span><span class="op">)</span></span> |
|
| 852 |
+<span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">normalise_list_rlm</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"matrix_antigen_rlm"</span>, <span class="st">"plot_rlm"</span><span class="op">)</span></span> |
|
| 853 |
+<span></span> |
|
| 854 |
+<span></span> |
|
| 855 |
+<span><span class="co">## create a list after normalisation</span></span> |
|
| 856 |
+<span><span class="va">normalised_list</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span> |
|
| 857 |
+<span> <span class="va">normalise_list_none</span>,</span> |
|
| 858 |
+<span> <span class="va">normalise_list_log</span>,</span> |
|
| 859 |
+<span> <span class="va">normalise_list_vsn</span>,</span> |
|
| 860 |
+<span> <span class="va">normalise_list_cyclic_loess_log</span>,</span> |
|
| 861 |
+<span> <span class="va">normalise_list_rlm</span></span> |
|
| 862 |
+<span><span class="op">)</span></span> |
|
| 863 |
+<span><span class="co">##</span></span> |
|
| 864 |
+<span><span class="va">normalised_list_plot</span> <span class="op"><-</span> <span class="va">normalised_list</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/grep.html" class="external-link">grepl</a></span><span class="op">(</span><span class="st">"plot"</span>, <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">normalised_list</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></span></code></pre></div> |
|
| 865 |
+<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r"> |
|
| 866 |
+<code class="sourceCode R"><span><span class="va">p</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/do.call.html" class="external-link">do.call</a></span><span class="op">(</span><span class="st">"grid.arrange"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">normalised_list_plot</span>, ncol <span class="op">=</span> <span class="fl">2</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> |
|
| 867 |
+<p><img src="vignette_files/figure-html/plot_comparison-1.png" width="1152" style="display: block; margin: auto;"></p> |
|
| 868 |
+</div> |
|
| 869 |
+</div> |
|
| 870 |
+<div class="section level2"> |
|
| 871 |
+<h2 id="heatmaps">Heatmaps<a class="anchor" aria-label="anchor" href="#heatmaps"></a> |
|
| 872 |
+</h2> |
|
| 873 |
+<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r"> |
|
| 874 |
+<code class="sourceCode R"><span><span class="va">norm_df</span> <span class="op"><-</span> <span class="va">normlise_df</span><span class="op">$</span><span class="va">matrix_antigen_normalised</span></span> |
|
| 875 |
+<span><span class="va">norm_df</span> <span class="op"><-</span> <span class="va">norm_df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span> |
|
| 876 |
+<span> <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">control_antigens</span><span class="op">)</span></span> |
|
| 877 |
+<span><span class="va">p3</span> <span class="op"><-</span> <span class="fu">pheatmap</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/pheatmap/man/pheatmap.html" class="external-link">pheatmap</a></span><span class="op">(</span><span class="va">norm_df</span>,</span> |
|
| 878 |
+<span> scale <span class="op">=</span> <span class="st">"none"</span>, cluster_rows <span class="op">=</span> <span class="cn">FALSE</span>,</span> |
|
| 879 |
+<span> main <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"VSN"</span>, <span class="st">"Normalised Data"</span><span class="op">)</span>,</span> |
|
| 880 |
+<span> silent <span class="op">=</span> <span class="cn">TRUE</span></span> |
|
| 881 |
+<span><span class="op">)</span></span> |
|
| 882 |
+<span><span class="co">#-------</span></span> |
|
| 883 |
+<span><span class="co">## if you want to save the file</span></span> |
|
| 884 |
+<span><span class="co"># p3 <- ggplotify::as.ggplot(p3)</span></span> |
|
| 885 |
+<span><span class="co"># p <- p3 + theme_void()</span></span> |
|
| 886 |
+<span><span class="co"># ggsave(p ,</span></span> |
|
| 887 |
+<span><span class="co"># filename ="heatmap.PNG" ,</span></span> |
|
| 888 |
+<span><span class="co"># width = 16 , height = 12 ,</span></span> |
|
| 889 |
+<span><span class="co"># limitsize = FALSE,</span></span> |
|
| 890 |
+<span><span class="co"># dpi=200 )</span></span> |
|
| 891 |
+<span><span class="co">#-------</span></span> |
|
| 892 |
+<span><span class="va">p3</span></span></code></pre></div> |
|
| 893 |
+<p><img src="vignette_files/figure-html/heat_norm-1.png" width="700" style="display: block; margin: auto;"></p> |
|
| 894 |
+</div> |
|
| 895 |
+<div class="section level2"> |
|
| 896 |
+<h2 id="pca-analysis">PCA analysis<a class="anchor" aria-label="anchor" href="#pca-analysis"></a> |
|
| 897 |
+</h2> |
|
| 898 |
+<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r"> |
|
| 899 |
+<code class="sourceCode R"><span><span class="va">norm_df</span> <span class="op"><-</span> <span class="va">normlise_df</span><span class="op">$</span><span class="va">matrix_antigen_normalised</span></span> |
|
| 900 |
+<span><span class="va">res_pca</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/prcomp.html" class="external-link">prcomp</a></span><span class="op">(</span><span class="va">norm_df</span>, scale <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> |
|
| 901 |
+<span><span class="va">var</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/factoextra/man/get_pca.html" class="external-link">get_pca_var</a></span><span class="op">(</span><span class="va">res_pca</span><span class="op">)</span></span> |
|
| 902 |
+<span><span class="va">vars_visualise</span> <span class="op"><-</span> <span class="fl">20</span></span> |
|
| 903 |
+<span><span class="co"># Visualize the PCA</span></span> |
|
| 904 |
+<span><span class="co">## individuals contributing to the PCA</span></span> |
|
| 905 |
+<span><span class="va">p1</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/factoextra/man/fviz_pca.html" class="external-link">fviz_pca_ind</a></span><span class="op">(</span><span class="va">res_pca</span>,</span> |
|
| 906 |
+<span> col.var <span class="op">=</span> <span class="st">"contrib"</span>, <span class="co"># Color by contributions to the PC</span></span> |
|
| 907 |
+<span> gradient.cols <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"#00AFBB"</span>, <span class="st">"#E7B800"</span>, <span class="st">"#FC4E07"</span><span class="op">)</span>,</span> |
|
| 908 |
+<span> repel <span class="op">=</span> <span class="cn">TRUE</span> <span class="co"># Avoid text overlapping</span></span> |
|
| 909 |
+<span><span class="op">)</span> <span class="op">+</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggtheme.html" class="external-link">theme_minimal</a></span><span class="op">(</span><span class="op">)</span></span> |
|
| 910 |
+<span></span> |
|
| 911 |
+<span><span class="co"># Select the top vars_visualise contributing variables</span></span> |
|
| 912 |
+<span><span class="va">p2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/factoextra/man/fviz_pca.html" class="external-link">fviz_pca_biplot</a></span><span class="op">(</span><span class="va">res_pca</span>,</span> |
|
| 913 |
+<span> label <span class="op">=</span> <span class="st">"var"</span>,</span> |
|
| 914 |
+<span> select.var <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>contrib <span class="op">=</span> <span class="va">vars_visualise</span><span class="op">)</span></span> |
|
| 915 |
+<span><span class="op">)</span> <span class="op">+</span></span> |
|
| 916 |
+<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggtheme.html" class="external-link">theme_minimal</a></span><span class="op">(</span><span class="op">)</span></span> |
|
| 917 |
+<span></span> |
|
| 918 |
+<span></span> |
|
| 919 |
+<span><span class="co"># Total cos2 of variables on Dim.1 and Dim.2</span></span> |
|
| 920 |
+<span><span class="va">p3</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/factoextra/man/fviz_cos2.html" class="external-link">fviz_cos2</a></span><span class="op">(</span><span class="va">res_pca</span>, choice <span class="op">=</span> <span class="st">"var"</span>, axes <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fl">2</span>, top <span class="op">=</span> <span class="va">vars_visualise</span><span class="op">)</span></span> |
|
| 921 |
+<span></span> |
|
| 922 |
+<span></span> |
|
| 923 |
+<span><span class="co"># Color by cos2 values: quality on the factor map</span></span> |
|
| 924 |
+<span><span class="va">p4</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/factoextra/man/fviz_pca.html" class="external-link">fviz_pca_var</a></span><span class="op">(</span><span class="va">res_pca</span>,</span> |
|
| 925 |
+<span> col.var <span class="op">=</span> <span class="st">"cos2"</span>,</span> |
|
| 926 |
+<span> gradient.cols <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"#00AFBB"</span>, <span class="st">"#E7B800"</span>, <span class="st">"#FC4E07"</span><span class="op">)</span>,</span> |
|
| 927 |
+<span> select.var <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>contrib <span class="op">=</span> <span class="va">vars_visualise</span><span class="op">)</span>,</span> |
|
| 928 |
+<span> repel <span class="op">=</span> <span class="cn">TRUE</span> <span class="co"># Avoid text overlapping</span></span> |
|
| 929 |
+<span><span class="op">)</span></span> |
|
| 930 |
+<span></span> |
|
| 931 |
+<span></span> |
|
| 932 |
+<span><span class="co">## combine the plots into one grid</span></span> |
|
| 933 |
+<span><span class="co">## combine the plots into one grid</span></span> |
|
| 934 |
+<span><span class="co">## combine the plots into one grid</span></span> |
|
| 935 |
+<span><span class="va">p_pca</span> <span class="op"><-</span> <span class="fu">gridExtra</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/gridExtra/man/arrangeGrob.html" class="external-link">grid.arrange</a></span><span class="op">(</span><span class="va">p1</span>, <span class="va">p2</span>, <span class="va">p3</span>, <span class="va">p4</span>, ncol <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></code></pre></div> |
|
| 936 |
+<p><img src="vignette_files/figure-html/pca-1.png" width="1536" style="display: block; margin: auto;"></p> |
|
| 937 |
+<div class="sourceCode" id="cb30"><pre class="downlit sourceCode r"> |
|
| 938 |
+<code class="sourceCode R"><span><span class="co">## If you want to save the file</span></span> |
|
| 939 |
+<span><span class="co"># ggsave(p_pca ,</span></span> |
|
| 940 |
+<span><span class="co"># filename ="p_pca.PNG" ,</span></span> |
|
| 941 |
+<span><span class="co"># width = 16 , height = 12 ,</span></span> |
|
| 942 |
+<span><span class="co"># units = "in",</span></span> |
|
| 943 |
+<span><span class="co"># limitsize = FALSE,</span></span> |
|
| 944 |
+<span><span class="co"># dpi=300)</span></span> |
|
| 945 |
+<span><span class="va">p_pca</span></span></code></pre></div> |
|
| 946 |
+<pre><code><span><span class="co">## TableGrob (2 x 2) "arrange": 4 grobs</span></span> |
|
| 947 |
+<span><span class="co">## z cells name grob</span></span> |
|
| 948 |
+<span><span class="co">## 1 1 (1-1,1-1) arrange gtable[layout]</span></span> |
|
| 949 |
+<span><span class="co">## 2 2 (1-1,2-2) arrange gtable[layout]</span></span> |
|
| 950 |
+<span><span class="co">## 3 3 (2-2,1-1) arrange gtable[layout]</span></span> |
|
| 951 |
+<span><span class="co">## 4 4 (2-2,2-2) arrange gtable[layout]</span></span></code></pre> |
|
| 952 |
+</div> |
|
| 953 |
+<div class="section level2"> |
|
| 954 |
+<h2 id="shiny-application">Shiny application<a class="anchor" aria-label="anchor" href="#shiny-application"></a> |
|
| 955 |
+</h2> |
|
| 956 |
+<p>Shiny is an R package that makes it easy to build interactive web |
|
| 957 |
+apps straight from R. protGear has a built in user-friendly Shiny |
|
| 958 |
+dashboard to assist in real-time processing and visualization. It |
|
| 959 |
+provides five sequential steps for handling a data table of fluorescent |
|
| 960 |
+intensities. The dashboard is launched as below from R or RStudio. To |
|
| 961 |
+Install R: Open an internet browser and go to www.r-project.org.</p> |
|
| 962 |
+<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r"> |
|
| 963 |
+<code class="sourceCode R"><span><span class="fu">protGear</span><span class="fu">::</span><span class="fu"><a href="../reference/launch_protGear_interactive.html">launch_protGear_interactive</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> |
|
| 964 |
+<div class="sourceCode" id="cb33"><pre class="downlit sourceCode r"> |
|
| 965 |
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/sessionInfo.html" class="external-link">sessionInfo</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> |
|
| 966 |
+<pre><code><span><span class="co">## R version 4.2.1 (2022-06-23 ucrt)</span></span> |
|
| 967 |
+<span><span class="co">## Platform: x86_64-w64-mingw32/x64 (64-bit)</span></span> |
|
| 968 |
+<span><span class="co">## Running under: Windows 10 x64 (build 19044)</span></span> |
|
| 969 |
+<span><span class="co">## </span></span> |
|
| 970 |
+<span><span class="co">## Matrix products: default</span></span> |
|
| 971 |
+<span><span class="co">## </span></span> |
|
| 972 |
+<span><span class="co">## locale:</span></span> |
|
| 973 |
+<span><span class="co">## [1] LC_COLLATE=English_United Kingdom.utf8 </span></span> |
|
| 974 |
+<span><span class="co">## [2] LC_CTYPE=English_United Kingdom.utf8 </span></span> |
|
| 975 |
+<span><span class="co">## [3] LC_MONETARY=English_United Kingdom.utf8</span></span> |
|
| 976 |
+<span><span class="co">## [4] LC_NUMERIC=C </span></span> |
|
| 977 |
+<span><span class="co">## [5] LC_TIME=English_United Kingdom.utf8 </span></span> |
|
| 978 |
+<span><span class="co">## </span></span> |
|
| 979 |
+<span><span class="co">## attached base packages:</span></span> |
|
| 980 |
+<span><span class="co">## [1] grid stats graphics grDevices utils datasets methods </span></span> |
|
| 981 |
+<span><span class="co">## [8] base </span></span> |
|
| 982 |
+<span><span class="co">## </span></span> |
|
| 983 |
+<span><span class="co">## other attached packages:</span></span> |
|
| 984 |
+<span><span class="co">## [1] protGear_1.0.0 vsn_3.64.0 Biobase_2.56.0 </span></span> |
|
| 985 |
+<span><span class="co">## [4] BiocGenerics_0.42.0 limma_3.52.4 tidyr_1.2.1 </span></span> |
|
| 986 |
+<span><span class="co">## [7] dplyr_1.0.10 remotes_2.4.2 ggplotify_0.1.0 </span></span> |
|
| 987 |
+<span><span class="co">## [10] GGally_2.1.2 rlang_1.0.6 magick_2.7.3 </span></span> |
|
| 988 |
+<span><span class="co">## [13] factoextra_1.0.7 FactoMineR_2.6 styler_1.8.1 </span></span> |
|
| 989 |
+<span><span class="co">## [16] knitr_1.40 png_0.1-7 gridExtra_2.3 </span></span> |
|
| 990 |
+<span><span class="co">## [19] kableExtra_1.3.4 data.table_1.14.4 pheatmap_1.0.12 </span></span> |
|
| 991 |
+<span><span class="co">## [22] scales_1.2.1 purrr_0.3.5 gtools_3.9.3 </span></span> |
|
| 992 |
+<span><span class="co">## [25] ggpubr_0.4.0 ggplot2_3.4.0 </span></span> |
|
| 993 |
+<span><span class="co">## </span></span> |
|
| 994 |
+<span><span class="co">## loaded via a namespace (and not attached):</span></span> |
|
| 995 |
+<span><span class="co">## [1] backports_1.4.1 systemfonts_1.0.4 plyr_1.8.8 </span></span> |
|
| 996 |
+<span><span class="co">## [4] lazyeval_0.2.2 shinydashboard_0.7.2 splines_4.2.1 </span></span> |
|
| 997 |
+<span><span class="co">## [7] GenomeInfoDb_1.32.4 TH.data_1.1-1 digest_0.6.30 </span></span> |
|
| 998 |
+<span><span class="co">## [10] flexdashboard_0.6.0 yulab.utils_0.0.5 htmltools_0.5.3 </span></span> |
|
| 999 |
+<span><span class="co">## [13] fansi_1.0.3 magrittr_2.0.3 memoise_2.0.1 </span></span> |
|
| 1000 |
+<span><span class="co">## [16] cluster_2.1.3 tzdb_0.3.0 readr_2.1.3 </span></span> |
|
| 1001 |
+<span><span class="co">## [19] Biostrings_2.64.1 annotate_1.74.0 Kendall_2.2.1 </span></span> |
|
| 1002 |
+<span><span class="co">## [22] R.utils_2.12.2 sandwich_3.0-2 svglite_2.1.0 </span></span> |
|
| 1003 |
+<span><span class="co">## [25] pkgdown_2.0.6 colorspace_2.0-3 blob_1.2.3 </span></span> |
|
| 1004 |
+<span><span class="co">## [28] rvest_1.0.3 ggrepel_0.9.2 textshaping_0.3.6 </span></span> |
|
| 1005 |
+<span><span class="co">## [31] xfun_0.34 RCurl_1.98-1.9 crayon_1.5.2 </span></span> |
|
| 1006 |
+<span><span class="co">## [34] jsonlite_1.8.3 genefilter_1.78.0 survival_3.3-1 </span></span> |
|
| 1007 |
+<span><span class="co">## [37] zoo_1.8-11 glue_1.6.2 gtable_0.3.1 </span></span> |
|
| 1008 |
+<span><span class="co">## [40] XVector_0.36.0 zlibbioc_1.42.0 emmeans_1.8.2 </span></span> |
|
| 1009 |
+<span><span class="co">## [43] webshot_0.5.4 R.cache_0.16.0 car_3.1-1 </span></span> |
|
| 1010 |
+<span><span class="co">## [46] abind_1.4-5 mvtnorm_1.1-3 DBI_1.1.3 </span></span> |
|
| 1011 |
+<span><span class="co">## [49] rstatix_0.7.1 Rcpp_1.0.9 viridisLite_0.4.1 </span></span> |
|
| 1012 |
+<span><span class="co">## [52] xtable_1.8-4 gridGraphics_0.5-1 flashClust_1.01-2 </span></span> |
|
| 1013 |
+<span><span class="co">## [55] bit_4.0.4 preprocessCore_1.58.0 stats4_4.2.1 </span></span> |
|
| 1014 |
+<span><span class="co">## [58] DT_0.26 htmlwidgets_1.5.4 httr_1.4.4 </span></span> |
|
| 1015 |
+<span><span class="co">## [61] RColorBrewer_1.1-3 ellipsis_0.3.2 farver_2.1.1 </span></span> |
|
| 1016 |
+<span><span class="co">## [64] pkgconfig_2.0.3 reshape_0.8.9 XML_3.99-0.12 </span></span> |
|
| 1017 |
+<span><span class="co">## [67] R.methodsS3_1.8.2 multcompView_0.1-8 sass_0.4.2 </span></span> |
|
| 1018 |
+<span><span class="co">## [70] utf8_1.2.2 labeling_0.4.2 tidyselect_1.2.0 </span></span> |
|
| 1019 |
+<span><span class="co">## [73] later_1.3.0 AnnotationDbi_1.58.0 munsell_0.5.0 </span></span> |
|
| 1020 |
+<span><span class="co">## [76] tools_4.2.1 cachem_1.0.6 cli_3.4.0 </span></span> |
|
| 1021 |
+<span><span class="co">## [79] generics_0.1.3 RSQLite_2.2.18 broom_1.0.1 </span></span> |
|
| 1022 |
+<span><span class="co">## [82] evaluate_0.18 stringr_1.4.1 fastmap_1.1.0 </span></span> |
|
| 1023 |
+<span><span class="co">## [85] yaml_2.3.6 ragg_1.2.4 bit64_4.0.5 </span></span> |
|
| 1024 |
+<span><span class="co">## [88] fs_1.5.2 KEGGREST_1.36.3 nlme_3.1-157 </span></span> |
|
| 1025 |
+<span><span class="co">## [91] mime_0.12 R.oo_1.25.0 leaps_3.1 </span></span> |
|
| 1026 |
+<span><span class="co">## [94] xml2_1.3.3 compiler_4.2.1 rstudioapi_0.14 </span></span> |
|
| 1027 |
+<span><span class="co">## [97] plotly_4.10.1 affyio_1.66.0 ggsignif_0.6.4 </span></span> |
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+<span><span class="co">## [100] tibble_3.1.8 bslib_0.4.1 stringi_1.7.8 </span></span> |
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+<span><span class="co">## [103] highr_0.9 desc_1.4.2 lattice_0.20-45 </span></span> |
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+<span><span class="co">## [106] Matrix_1.5-3 vctrs_0.5.0 pillar_1.8.1 </span></span> |
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+<span><span class="co">## [109] lifecycle_1.0.3 BiocManager_1.30.19 jquerylib_0.1.4 </span></span> |
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+<span><span class="co">## [112] estimability_1.4.1 bitops_1.0-7 httpuv_1.6.6 </span></span> |
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+<span><span class="co">## [115] R6_2.5.1 affy_1.74.0 promises_1.2.0.1 </span></span> |
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+<span><span class="co">## [118] IRanges_2.30.1 codetools_0.2-18 boot_1.3-28 </span></span> |
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+<span><span class="co">## [121] MASS_7.3-58.1 assertthat_0.2.1 rprojroot_2.0.3 </span></span> |
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+<span><span class="co">## [124] withr_2.5.0 GenomeInfoDbData_1.2.8 S4Vectors_0.34.0 </span></span> |
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+<span><span class="co">## [127] multcomp_1.4-20 mgcv_1.8-40 hms_1.1.2 </span></span> |
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+<span><span class="co">## [130] rmarkdown_2.18 carData_3.0-5 scatterplot3d_0.3-42 </span></span> |
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+<span><span class="co">## [133] shiny_1.7.3</span></span></code></pre> |
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+</div> |
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+ </div> |
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+ |
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+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |
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+ |
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+ <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2> |
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+ </nav> |
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+</div> |
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+ |
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+</div> |
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+ |
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+ |
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+ <footer><div class="copyright"> |
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+ <p></p> |
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+<p>Developed by Kennedy Mwai, James Mburu.</p> |
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+</div> |
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+ |
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+<div class="pkgdown"> |
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+ <p></p> |
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+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> |
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+<!DOCTYPE html> |
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Authors and Citation • protGear</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="bootstrap-toc.css"><script src="bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"><script src="pkgdown.js"></script><meta property="og:title" content="Authors and Citation"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> |
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+ <a class="navbar-link" href="index.html">protGear</a> |
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+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.2.1</span> |
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+ <a href="articles/vignette.html">protGear vignette processing suite</a> |
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+ </ul></li> |
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+<li> |
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+ <a href="news/index.html">Changelog</a> |
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+</li> |
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+ </ul><ul class="nav navbar-nav navbar-right"><li> |
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+ |
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+ </header><div class="row"> |
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+ <div class="contents col-md-9"> |
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+ <div class="section level2 authors-section"> |
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+ <div class="page-header"> |
|
| 57 |
+ <h1>Authors</h1> |
|
| 58 |
+ </div> |
|
| 59 |
+ |
|
| 60 |
+ |
|
| 61 |
+ <ul class="list-unstyled"><li> |
|
| 62 |
+ <p><strong>Kennedy Mwai</strong>. Maintainer, author. |
|
| 63 |
+ </p> |
|
| 64 |
+ </li> |
|
| 65 |
+ <li> |
|
| 66 |
+ <p><strong>James Mburu</strong>. Author. |
|
| 67 |
+ </p> |
|
| 68 |
+ </li> |
|
| 69 |
+ <li> |
|
| 70 |
+ <p><strong>Jacqueline Waeni</strong>. Contributor. |
|
| 71 |
+ </p> |
|
| 72 |
+ </li> |
|
| 73 |
+ </ul></div> |
|
| 74 |
+ <div class="section level2 citation-section"> |
|
| 75 |
+ <div> |
|
| 76 |
+ <h1 id="citation">Citation</h1> |
|
| 77 |
+ <small class="dont-index">Source: <a href="https://github.com/Keniajin/protGear/blob/HEAD/DESCRIPTION" class="external-link"><code>DESCRIPTION</code></a></small> |
|
| 78 |
+ </div> |
|
| 79 |
+ </div> |
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| 80 |
+ |
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| 81 |
+ |
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| 82 |
+ <p>Mwai K, James |
|
| 83 |
+Mburu (2022). |
|
| 84 |
+<em>protGear: Protein Micro Array Data Management and Interactive Visualization</em>. |
|
| 85 |
+R package version 1.2.1, <a href="https://github.com/Keniajin/protGear" class="external-link">https://github.com/Keniajin/protGear</a>. |
|
| 86 |
+</p> |
|
| 87 |
+ <pre>@Manual{,
|
|
| 88 |
+ title = {protGear: Protein Micro Array Data Management and Interactive Visualization},
|
|
| 89 |
+ author = {Kennedy Mwai and {James Mburu}},
|
|
| 90 |
+ year = {2022},
|
|
| 91 |
+ note = {R package version 1.2.1},
|
|
| 92 |
+ url = {https://github.com/Keniajin/protGear},
|
|
| 93 |
+}</pre> |
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+ |
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+ </div> |
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+ |
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+</div> |
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+ |
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+ |
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+ |
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+ <footer><div class="copyright"> |
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+ <p></p><p>Developed by Kennedy Mwai, James Mburu.</p> |
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+</div> |
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+ |
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+<div class="pkgdown"> |
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+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> |
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+ </footer></div> |
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+ |
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+ </body></html> |
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+ |
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+<!DOCTYPE html> |
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"> |
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+<head> |
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+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> |
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+<meta charset="utf-8"> |
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+<meta http-equiv="X-UA-Compatible" content="IE=edge"> |
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+<meta name="viewport" content="width=device-width, initial-scale=1.0"> |
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+<title>Protein Micro Array Data Management and Interactive Visualization • protGear</title> |
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+<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"> |
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+<script src="bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"> |
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+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"> |
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+<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"> |
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+<script src="pkgdown.js"></script><meta property="og:title" content="Protein Micro Array Data Management and Interactive Visualization"> |
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+<meta property="og:description" content="A generic three-step pre-processing package for protein microarray data. This package contains different data pre-processing procedures to allow comparison of their performance.These steps are background correction, the coefficient of variation (CV) based filtering, batch correction and normalization."> |
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| 16 |
+<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> |
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+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> |
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+<![endif]--> |
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+</head> |
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+<body data-spy="scroll" data-target="#toc"> |
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+ <div class="container template-home"> |
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+ <a class="navbar-link" href="index.html">protGear</a> |
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+<li> |
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+ <a href="articles/vignette.html">protGear vignette processing suite</a> |
|
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+ </li> |
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+ </ul> |
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+</li> |
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+<li> |
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+ <a href="news/index.html">Changelog</a> |
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+</li> |
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+ </ul> |
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+<ul class="nav navbar-nav navbar-right"> |
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+<li> |
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+ <a href="https://github.com/Keniajin/protGear/" class="external-link"> |
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+ <span class="fab fa-github fa-lg"></span> |
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+ |
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+ </a> |
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+</li> |
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+ </ul> |
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+</div> |
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+<!--/.nav-collapse --> |
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+ </div> |
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+<!--/.container --> |
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+</div> |
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+<!--/.navbar --> |
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+ |
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+ |
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+ |
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| 78 |
+ </header><div class="row"> |
|
| 79 |
+ <div class="contents col-md-9"> |
|
| 80 |
+ |
|
| 81 |
+<div class="section level2"> |
|
| 82 |
+<h2 id="general-information">General information<a class="anchor" aria-label="anchor" href="#general-information"></a> |
|
| 83 |
+</h2> |
|
| 84 |
+<p>protGear is a package for protein micro-array data processing just before the main analysis.</p> |
|
| 85 |
+<p>The package loads the ‘<code>gpr</code>’ or ‘<code>txt</code>’ file format extracted by the quantification software and merges this with the specific sample identifiers. The package processes multiple files extracted in a batch with their corresponding sample identifier file. The sample identifier file has 2 variables ‘<code>v1</code>’ and ‘<code>v2</code>’ which indicate the mini-array or block number and sample identifier respectively. The ‘<code>gpr</code>’ file and the corresponding sample identifier file have the same file name. protGear also provides a web based <span class="math inline"><em>S</em><em>h</em><em>i</em><em>n</em><em>y</em><sup>(<em>R</em>)</sup></span> platform for real time visualization of the data processing.</p> |
|
| 86 |
+<p>There is a package vignette included with this package with a step by step use of the package. Check <a href="https://keniajin.github.io/protGear/" class="external-link uri">https://keniajin.github.io/protGear/</a> under articles.</p> |
|
| 87 |
+</div> |
|
| 88 |
+<div class="section level2"> |
|
| 89 |
+<h2 id="installing-the-devel-package">Installing the devel package<a class="anchor" aria-label="anchor" href="#installing-the-devel-package"></a> |
|
| 90 |
+</h2> |
|
| 91 |
+<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> |
|
| 92 |
+<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://remotes.r-lib.org" class="external-link">remotes</a></span><span class="op">)</span> </span> |
|
| 93 |
+<span><span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"keniajin/protGear"</span><span class="op">)</span></span></code></pre></div> |
|
| 94 |
+</div> |
|
| 95 |
+<div class="section level2"> |
|
| 96 |
+<h2 id="installing-from-bioc-bioconductor">Installing from Bioc BioConductor<a class="anchor" aria-label="anchor" href="#installing-from-bioc-bioconductor"></a> |
|
| 97 |
+</h2> |
|
| 98 |
+<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> |
|
| 99 |
+<code class="sourceCode R"><span><span class="co">## install from BioConductor</span></span> |
|
| 100 |
+<span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st">"BiocManager"</span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span>
|
|
| 101 |
+<span> <span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"BiocManager"</span><span class="op">)</span></span> |
|
| 102 |
+<span><span class="op">}</span></span> |
|
| 103 |
+<span><span class="fu">BiocManager</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/BiocManager/man/install.html" class="external-link">install</a></span><span class="op">(</span><span class="st">"protGear"</span><span class="op">)</span></span></code></pre></div> |
|
| 104 |
+</div> |
|
| 105 |
+<div class="section level2"> |
|
| 106 |
+<h2 id="to-run-the-shiny-application">To run the shiny application<a class="anchor" aria-label="anchor" href="#to-run-the-shiny-application"></a> |
|
| 107 |
+</h2> |
|
| 108 |
+<p>To use the application locally on your compute install R and launch the app using the following command. <code><a href="reference/launch_protGear_interactive.html">protGear::launch_protGear_interactive()</a></code></p> |
|
| 109 |
+<p>To Install R: - Open an Internet browser and go to www.r-project.org. - Under “Getting Started” click the “download R” link - Select a CRAN location (a mirror site) and click the corresponding link. - Download R depending on your operating system.</p> |
|
| 110 |
+</div> |
|
| 111 |
+<div class="section level2"> |
|
| 112 |
+<h2 id="protgear-help-pages">protGear help pages<a class="anchor" aria-label="anchor" href="#protgear-help-pages"></a> |
|
| 113 |
+</h2> |
|
| 114 |
+<ul> |
|
| 115 |
+<li>The main page - <a href="https://keniajin.github.io/protGear/" class="external-link uri">https://keniajin.github.io/protGear/</a> |
|
| 116 |
+</li> |
|
| 117 |
+<li>Vignette - <a href="https://keniajin.github.io/protGear/articles/vignette.html" class="external-link uri">https://keniajin.github.io/protGear/articles/vignette.html</a> |
|
| 118 |
+</li> |
|
| 119 |
+</ul> |
|
| 120 |
+</div> |
|
| 121 |
+<div class="section level2"> |
|
| 122 |
+<h2 id="contribute">Contribute<a class="anchor" aria-label="anchor" href="#contribute"></a> |
|
| 123 |
+</h2> |
|
| 124 |
+<p>Check the Github page for <a href="https://github.com/Keniajin/protGear/" class="external-link">source code</a>.</p> |
|
| 125 |
+</div> |
|
| 126 |
+<div class="section level2"> |
|
| 127 |
+<h2 id="publication">Publication<a class="anchor" aria-label="anchor" href="#publication"></a> |
|
| 128 |
+</h2> |
|
| 129 |
+<p>Mwai K, Kibinge N, Tuju J, Kamuyu G, Kimathi R, Mburu J, Chepsat E, Nyamako L, Chege T, Nkumama I, Kinyanjui S. et al. , protGear: A protein microarray data pre-processing suite. Computational and Structural Biotechnology Journal. 2021 Apr 24.</p> |
|
| 130 |
+<p>DOI: <a href="https://doi.org/10.1016/j.csbj.2021.04.044" class="external-link uri">https://doi.org/10.1016/j.csbj.2021.04.044</a></p> |
|
| 131 |
+</div> |
|
| 132 |
+ |
|
| 133 |
+ </div> |
|
| 134 |
+ |
|
| 135 |
+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |
|
| 136 |
+ <div class="links"> |
|
| 137 |
+<h2 data-toc-skip>Links</h2> |
|
| 138 |
+<ul class="list-unstyled"> |
|
| 139 |
+<li><a href="https://www.bioconductor.org/packages/protGear" class="external-link">View on Bioconductor</a></li> |
|
| 140 |
+<li><a href="https://github.com/Keniajin/protGear/" class="external-link">Browse source code</a></li> |
|
| 141 |
+<li><a href="https://github.com/Keniajin/protGear/issues" class="external-link">Report a bug</a></li> |
|
| 142 |
+</ul> |
|
| 143 |
+</div> |
|
| 144 |
+ |
|
| 145 |
+<div class="license"> |
|
| 146 |
+<h2 data-toc-skip>License</h2> |
|
| 147 |
+<ul class="list-unstyled"> |
|
| 148 |
+<li><a href="https://www.r-project.org/Licenses/GPL-3" class="external-link">GPL-3</a></li> |
|
| 149 |
+</ul> |
|
| 150 |
+</div> |
|
| 151 |
+ |
|
| 152 |
+ |
|
| 153 |
+<div class="citation"> |
|
| 154 |
+<h2 data-toc-skip>Citation</h2> |
|
| 155 |
+<ul class="list-unstyled"> |
|
| 156 |
+<li><a href="authors.html#citation">Citing protGear</a></li> |
|
| 157 |
+</ul> |
|
| 158 |
+</div> |
|
| 159 |
+ |
|
| 160 |
+<div class="developers"> |
|
| 161 |
+<h2 data-toc-skip>Developers</h2> |
|
| 162 |
+<ul class="list-unstyled"> |
|
| 163 |
+<li>Kennedy Mwai <br><small class="roles"> Maintainer, author </small> </li> |
|
| 164 |
+<li>James Mburu <br><small class="roles"> Author </small> </li> |
|
| 165 |
+<li><a href="authors.html">More about authors...</a></li> |
|
| 166 |
+</ul> |
|
| 167 |
+</div> |
|
| 168 |
+ |
|
| 169 |
+ |
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| 170 |
+ |
|
| 171 |
+ </div> |
|
| 172 |
+</div> |
|
| 173 |
+ |
|
| 174 |
+ |
|
| 175 |
+ <footer><div class="copyright"> |
|
| 176 |
+ <p></p> |
|
| 177 |
+<p>Developed by Kennedy Mwai, James Mburu.</p> |
|
| 178 |
+</div> |
|
| 179 |
+ |
|
| 180 |
+<div class="pkgdown"> |
|
| 181 |
+ <p></p> |
|
| 182 |
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> |
|
| 183 |
+</div> |
|
| 184 |
+ |
|
| 185 |
+ </footer> |
|
| 186 |
+</div> |
|
| 187 |
+ |
|
| 188 |
+ |
|
| 189 |
+ |
|
| 190 |
+ |
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+ |
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+ |
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+ </body> |
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+</html> |
| 0 | 195 |
new file mode 100644 |
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| 1 |
+<!DOCTYPE html> |
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Changelog • protGear</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Changelog"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> |
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+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> |
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+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> |
|
| 5 |
+<![endif]--></head><body data-spy="scroll" data-target="#toc"> |
|
| 6 |
+ |
|
| 7 |
+ |
|
| 8 |
+ <div class="container template-news"> |
|
| 9 |
+ <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> |
|
| 10 |
+ <div class="container"> |
|
| 11 |
+ <div class="navbar-header"> |
|
| 12 |
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> |
|
| 13 |
+ <span class="sr-only">Toggle navigation</span> |
|
| 14 |
+ <span class="icon-bar"></span> |
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+ <span class="icon-bar"></span> |
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+ <span class="icon-bar"></span> |
|
| 17 |
+ </button> |
|
| 18 |
+ <span class="navbar-brand"> |
|
| 19 |
+ <a class="navbar-link" href="../index.html">protGear</a> |
|
| 20 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.2.1</span> |
|
| 21 |
+ </span> |
|
| 22 |
+ </div> |
|
| 23 |
+ |
|
| 24 |
+ <div id="navbar" class="navbar-collapse collapse"> |
|
| 25 |
+ <ul class="nav navbar-nav"><li> |
|
| 26 |
+ <a href="../reference/index.html">Reference</a> |
|
| 27 |
+</li> |
|
| 28 |
+<li class="dropdown"> |
|
| 29 |
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> |
|
| 30 |
+ Articles |
|
| 31 |
+ |
|
| 32 |
+ <span class="caret"></span> |
|
| 33 |
+ </a> |
|
| 34 |
+ <ul class="dropdown-menu" role="menu"><li> |
|
| 35 |
+ <a href="../articles/vignette.html">protGear vignette processing suite</a> |
|
| 36 |
+ </li> |
|
| 37 |
+ </ul></li> |
|
| 38 |
+<li> |
|
| 39 |
+ <a href="../news/index.html">Changelog</a> |
|
| 40 |
+</li> |
|
| 41 |
+ </ul><ul class="nav navbar-nav navbar-right"><li> |
|
| 42 |
+ <a href="https://github.com/Keniajin/protGear/" class="external-link"> |
|
| 43 |
+ <span class="fab fa-github fa-lg"></span> |
|
| 44 |
+ |
|
| 45 |
+ </a> |
|
| 46 |
+</li> |
|
| 47 |
+ </ul></div><!--/.nav-collapse --> |
|
| 48 |
+ </div><!--/.container --> |
|
| 49 |
+</div><!--/.navbar --> |
|
| 50 |
+ |
|
| 51 |
+ |
|
| 52 |
+ |
|
| 53 |
+ </header><div class="row"> |
|
| 54 |
+ <div class="col-md-9 contents"> |
|
| 55 |
+ <div class="page-header"> |
|
| 56 |
+ <h1 data-toc-skip>Changelog <small></small></h1> |
|
| 57 |
+ <small>Source: <a href="https://github.com/Keniajin/protGear/blob/HEAD/NEWS.md" class="external-link"><code>NEWS.md</code></a></small> |
|
| 58 |
+ </div> |
|
| 59 |
+ |
|
| 60 |
+ <div class="section level2"> |
|
| 61 |
+<h2 class="page-header" data-toc-text="development version" id="protgear-development-version">protGear (development version)<a class="anchor" aria-label="anchor" href="#protgear-development-version"></a></h2> |
|
| 62 |
+<ul><li>Devel version</li> |
|
| 63 |
+</ul></div> |
|
| 64 |
+ <div class="section level2"> |
|
| 65 |
+<h2 class="page-header" data-toc-text="0.99.1" id="protgear-0991-2021-12-15">protGear 0.99.1 (2021-12-15)<a class="anchor" aria-label="anchor" href="#protgear-0991-2021-12-15"></a></h2> |
|
| 66 |
+<ul><li>Submitted to Bioconductor</li> |
|
| 67 |
+</ul></div> |
|
| 68 |
+ <div class="section level2"> |
|
| 69 |
+<h2 class="page-header" data-toc-text="0.99.543" id="protgear-099543-2022-02-14">protGear 0.99.543 (2022-02-14)<a class="anchor" aria-label="anchor" href="#protgear-099543-2022-02-14"></a></h2> |
|
| 70 |
+<ul><li>Submitted to Bioconductor for review</li> |
|
| 71 |
+</ul></div> |
|
| 72 |
+ <div class="section level2"> |
|
| 73 |
+<h2 class="page-header" data-toc-text="0.99.544" id="protgear-099544-2022-03-17">protGear 0.99.544 (2022-03-17)<a class="anchor" aria-label="anchor" href="#protgear-099544-2022-03-17"></a></h2> |
|
| 74 |
+<ul><li>Removed non Bioconductor files</li> |
|
| 75 |
+<li>Added Suggests in Description</li> |
|
| 76 |
+<li>Updated R requirement to 4.2</li> |
|
| 77 |
+<li>Added the data documentation</li> |
|
| 78 |
+</ul></div> |
|
| 79 |
+ <div class="section level2"> |
|
| 80 |
+<h2 class="page-header" data-toc-text="0.99.545" id="protgear-099545-2022-03-23">protGear 0.99.545 (2022-03-23)<a class="anchor" aria-label="anchor" href="#protgear-099545-2022-03-23"></a></h2> |
|
| 81 |
+<ul><li>Updated the NEWS file</li> |
|
| 82 |
+<li>Removed other non Bioconductor files</li> |
|
| 83 |
+</ul></div> |
|
| 84 |
+ <div class="section level2"> |
|
| 85 |
+<h2 class="page-header" data-toc-text="0.99.546" id="protgear-099546-2022-03-25">protGear 0.99.546 (2022-03-25)<a class="anchor" aria-label="anchor" href="#protgear-099546-2022-03-25"></a></h2> |
|
| 86 |
+<ul><li>Updated the shiny app path</li> |
|
| 87 |
+<li>Added Bioconductor installation in the app</li> |
|
| 88 |
+</ul></div> |
|
| 89 |
+ <div class="section level2"> |
|
| 90 |
+<h2 class="page-header" data-toc-text="0.99.55" id="protgear-09955-2022-04-08">protGear 0.99.55 (2022-04-08)<a class="anchor" aria-label="anchor" href="#protgear-09955-2022-04-08"></a></h2> |
|
| 91 |
+<ul><li>removed vignette.R and csv file</li> |
|
| 92 |
+</ul></div> |
|
| 93 |
+ <div class="section level2"> |
|
| 94 |
+<h2 class="page-header" data-toc-text="1.3.0" id="protgear-130-2022-11-15">protGear 1.3.0 (2022-11-15)<a class="anchor" aria-label="anchor" href="#protgear-130-2022-11-15"></a></h2> |
|
| 95 |
+<ul><li>Updated shiny app to load</li> |
|
| 96 |
+<li>Added missing paths for launch_protGear_interactive</li> |
|
| 97 |
+</ul></div> |
|
| 98 |
+ </div> |
|
| 99 |
+ |
|
| 100 |
+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |
|
| 101 |
+ <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> |
|
| 102 |
+ </nav></div> |
|
| 103 |
+ |
|
| 104 |
+</div> |
|
| 105 |
+ |
|
| 106 |
+ |
|
| 107 |
+ <footer><div class="copyright"> |
|
| 108 |
+ <p></p><p>Developed by Kennedy Mwai, James Mburu.</p> |
|
| 109 |
+</div> |
|
| 110 |
+ |
|
| 111 |
+<div class="pkgdown"> |
|
| 112 |
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> |
|
| 113 |
+</div> |
|
| 114 |
+ |
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| 115 |
+ </footer></div> |
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+ |
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+ |
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+ |
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+ |
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+ |
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+ |
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+ </body></html> |
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+ |
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+ <div class="col-md-9 contents"> |
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+ <div class="page-header"> |
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+ <h1>List the array structure variables</h1> |
|
| 57 |
+ <small class="dont-index">Source: <a href="https://github.com/Keniajin/protGear/blob/HEAD/R/global_functions.R" class="external-link"><code>R/global_functions.R</code></a></small> |
|
| 58 |
+ <div class="hidden name"><code>array_vars.Rd</code></div> |
|
| 59 |
+ </div> |
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+ |
|
| 61 |
+ <div class="ref-description"> |
|
| 62 |
+ <p>A generic function returning a list with the data structure.</p> |
|
| 63 |
+ </div> |
|
| 64 |
+ |
|
| 65 |
+ <div id="ref-usage"> |
|
| 66 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">array_vars</span><span class="op">(</span></span> |
|
| 67 |
+<span> channel <span class="op">=</span> <span class="st">"635"</span>,</span> |
|
| 68 |
+<span> <span class="va">totsamples</span>,</span> |
|
| 69 |
+<span> FG <span class="op">=</span> <span class="st">""</span>,</span> |
|
| 70 |
+<span> BG <span class="op">=</span> <span class="st">""</span>,</span> |
|
| 71 |
+<span> FBG <span class="op">=</span> <span class="st">""</span>,</span> |
|
| 72 |
+<span> <span class="va">blockspersample</span>,</span> |
|
| 73 |
+<span> chip_path <span class="op">=</span> <span class="st">"data/array_data"</span>,</span> |
|
| 74 |
+<span> sampleID_path <span class="op">=</span> <span class="st">"data/array_sampleID/"</span>,</span> |
|
| 75 |
+<span> mig_prefix <span class="op">=</span> <span class="st">"_first"</span>,</span> |
|
| 76 |
+<span> machine <span class="op">=</span> <span class="st">""</span>,</span> |
|
| 77 |
+<span> date_process <span class="op">=</span> <span class="st">""</span></span> |
|
| 78 |
+<span><span class="op">)</span></span></code></pre></div> |
|
| 79 |
+ </div> |
|
| 80 |
+ |
|
| 81 |
+ <div id="arguments"> |
|
| 82 |
+ <h2>Arguments</h2> |
|
| 83 |
+ <dl><dt>channel</dt> |
|
| 84 |
+<dd><p>A character indicating the channel that the data was scanned |
|
| 85 |
+at. It is mostly included in the MFI variable names.</p></dd> |
|
| 86 |
+ |
|
| 87 |
+ |
|
| 88 |
+<dt>totsamples</dt> |
|
| 89 |
+<dd><p>A numeric value indicating teh number of samples on a slide.</p></dd> |
|
| 90 |
+ |
|
| 91 |
+ |
|
| 92 |
+<dt>FG</dt> |
|
| 93 |
+<dd><p>Optional:A character indicating the name of the foreground |
|
| 94 |
+variable name. if not specified its created as |
|
| 95 |
+<code>paste0("F",channel,".Median")</code></p></dd>
|
|
| 96 |
+ |
|
| 97 |
+ |
|
| 98 |
+<dt>BG</dt> |
|
| 99 |
+<dd><p>Optional:A character indicating the name of the background |
|
| 100 |
+variable name. if not specified its created as |
|
| 101 |
+<code>paste0("B",channel,".Median")</code></p></dd>
|
|
| 102 |
+ |
|
| 103 |
+ |
|
| 104 |
+<dt>FBG</dt> |
|
| 105 |
+<dd><p>Optional:A character indicating the name of the |
|
| 106 |
+foreground - background variable name. if not specified its |
|
| 107 |
+created as <code>paste0("F",channel,".Median...B",channel)</code></p></dd>
|
|
| 108 |
+ |
|
| 109 |
+ |
|
| 110 |
+<dt>blockspersample</dt> |
|
| 111 |
+<dd><p>A numeric value indicating the numer of blocks in a |
|
| 112 |
+mini-array. The <code>".gal"</code> file can help in getting this</p></dd> |
|
| 113 |
+ |
|
| 114 |
+ |
|
| 115 |
+<dt>chip_path</dt> |
|
| 116 |
+<dd><p>A character indicating the path of the folder location with |
|
| 117 |
+the array data.</p></dd> |
|
| 118 |
+ |
|
| 119 |
+ |
|
| 120 |
+<dt>sampleID_path</dt> |
|
| 121 |
+<dd><p>A character indicating the path of the folder location |
|
| 122 |
+with the sample identifiers matching the array structure.</p></dd> |
|
| 123 |
+ |
|
| 124 |
+ |
|
| 125 |
+<dt>mig_prefix</dt> |
|
| 126 |
+<dd><p>Optional: A character indicating the identifier of an MIG |
|
| 127 |
+dilution file</p></dd> |
|
| 128 |
+ |
|
| 129 |
+ |
|
| 130 |
+<dt>machine</dt> |
|
| 131 |
+<dd><p>Optional:A character indicating the machine used to process |
|
| 132 |
+the data in the folder</p></dd> |
|
| 133 |
+ |
|
| 134 |
+ |
|
| 135 |
+<dt>date_process</dt> |
|
| 136 |
+<dd><p>Optional:A character indicating the date |
|
| 137 |
+when the samples were processed.</p></dd> |
|
| 138 |
+ |
|
| 139 |
+</dl></div> |
|
| 140 |
+ <div id="value"> |
|
| 141 |
+ <h2>Value</h2> |
|
| 142 |
+ |
|
| 143 |
+ |
|
| 144 |
+<p>a list of parameters required to process the data</p> |
|
| 145 |
+ |
|
| 146 |
+ |
|
| 147 |
+<p>genepix_vars</p> |
|
| 148 |
+ </div> |
|
| 149 |
+ |
|
| 150 |
+ <div id="ref-examples"> |
|
| 151 |
+ <h2>Examples</h2> |
|
| 152 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co">## specify the the parameters to process the data</span></span></span> |
|
| 153 |
+<span class="r-in"><span><span class="va">genepix_vars</span> <span class="op"><-</span> <span class="fu">array_vars</span><span class="op">(</span></span></span> |
|
| 154 |
+<span class="r-in"><span><span class="co">## the channel the data was processed in</span></span></span> |
|
| 155 |
+<span class="r-in"><span> channel <span class="op">=</span> <span class="st">"635"</span>,</span></span> |
|
| 156 |
+<span class="r-in"><span> <span class="co">## folder where the array data is stored</span></span></span> |
|
| 157 |
+<span class="r-in"><span> chip_path <span class="op">=</span> <span class="st">"data/array_data"</span>,</span></span> |
|
| 158 |
+<span class="r-in"><span> <span class="co">## the number of samples per slide or in as single run</span></span></span> |
|
| 159 |
+<span class="r-in"><span> totsamples <span class="op">=</span> <span class="fl">21</span>,</span></span> |
|
| 160 |
+<span class="r-in"><span> <span class="co">## How many blocks each sample occupies</span></span></span> |
|
| 161 |
+<span class="r-in"><span> blockspersample <span class="op">=</span> <span class="fl">2</span>,</span></span> |
|
| 162 |
+<span class="r-in"><span> <span class="co">## folder where the array data samples id files are stored</span></span></span> |
|
| 163 |
+<span class="r-in"><span> sampleID_path <span class="op">=</span> <span class="st">"data/array_sampleID/"</span>,</span></span> |
|
| 164 |
+<span class="r-in"><span> <span class="co">## optional</span></span></span> |
|
| 165 |
+<span class="r-in"><span> mig_prefix <span class="op">=</span> <span class="st">"_first"</span>,</span></span> |
|
| 166 |
+<span class="r-in"><span> machine <span class="op">=</span> <span class="fl">1</span>,</span></span> |
|
| 167 |
+<span class="r-in"><span> date_process <span class="op">=</span> <span class="st">"0520"</span></span></span> |
|
| 168 |
+<span class="r-in"><span><span class="op">)</span></span></span> |
|
| 169 |
+<span class="r-in"><span><span class="va">genepix_vars</span></span></span> |
|
| 170 |
+<span class="r-out co"><span class="r-pr">#></span> $FG</span> |
|
| 171 |
+<span class="r-out co"><span class="r-pr">#></span> F635.Median</span> |
|
| 172 |
+<span class="r-out co"><span class="r-pr">#></span> </span> |
|
| 173 |
+<span class="r-out co"><span class="r-pr">#></span> $BG</span> |
|
| 174 |
+<span class="r-out co"><span class="r-pr">#></span> B635.Median</span> |
|
| 175 |
+<span class="r-out co"><span class="r-pr">#></span> </span> |
|
| 176 |
+<span class="r-out co"><span class="r-pr">#></span> $FBG</span> |
|
| 177 |
+<span class="r-out co"><span class="r-pr">#></span> F635.Median...B635</span> |
|
| 178 |
+<span class="r-out co"><span class="r-pr">#></span> </span> |
|
| 179 |
+<span class="r-out co"><span class="r-pr">#></span> $paths</span> |
|
| 180 |
+<span class="r-out co"><span class="r-pr">#></span> character(0)</span> |
|
| 181 |
+<span class="r-out co"><span class="r-pr">#></span> </span> |
|
| 182 |
+<span class="r-out co"><span class="r-pr">#></span> $chip_path</span> |
|
| 183 |
+<span class="r-out co"><span class="r-pr">#></span> [1] "data/array_data"</span> |
|
| 184 |
+<span class="r-out co"><span class="r-pr">#></span> </span> |
|
| 185 |
+<span class="r-out co"><span class="r-pr">#></span> $sampleID_path</span> |
|
| 186 |
+<span class="r-out co"><span class="r-pr">#></span> [1] "data/array_sampleID/"</span> |
|
| 187 |
+<span class="r-out co"><span class="r-pr">#></span> </span> |
|
| 188 |
+<span class="r-out co"><span class="r-pr">#></span> $mig_prefix</span> |
|
| 189 |
+<span class="r-out co"><span class="r-pr">#></span> [1] "_first"</span> |
|
| 190 |
+<span class="r-out co"><span class="r-pr">#></span> </span> |
|
| 191 |
+<span class="r-out co"><span class="r-pr">#></span> $machine</span> |
|
| 192 |
+<span class="r-out co"><span class="r-pr">#></span> [1] 1</span> |
|
| 193 |
+<span class="r-out co"><span class="r-pr">#></span> </span> |
|
| 194 |
+<span class="r-out co"><span class="r-pr">#></span> $date_process</span> |
|
| 195 |
+<span class="r-out co"><span class="r-pr">#></span> [1] "0520"</span> |
|
| 196 |
+<span class="r-out co"><span class="r-pr">#></span> </span> |
|
| 197 |
+<span class="r-out co"><span class="r-pr">#></span> $totsamples</span> |
|
| 198 |
+<span class="r-out co"><span class="r-pr">#></span> [1] 21</span> |
|
| 199 |
+<span class="r-out co"><span class="r-pr">#></span> </span> |
|
| 200 |
+<span class="r-out co"><span class="r-pr">#></span> $blockspersample</span> |
|
| 201 |
+<span class="r-out co"><span class="r-pr">#></span> [1] 2</span> |
|
| 202 |
+<span class="r-out co"><span class="r-pr">#></span> </span> |
|
| 203 |
+<span class="r-out co"><span class="r-pr">#></span> $mp</span> |
|
| 204 |
+<span class="r-out co"><span class="r-pr">#></span> [1] 1</span> |
|
| 205 |
+<span class="r-out co"><span class="r-pr">#></span> </span> |
|
| 206 |
+<span class="r-out co"><span class="r-pr">#></span> $dp</span> |
|
| 207 |
+<span class="r-out co"><span class="r-pr">#></span> [1] "0520"</span> |
|
| 208 |
+<span class="r-out co"><span class="r-pr">#></span> </span> |
|
| 209 |
+</code></pre></div> |
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+ <div class="col-md-9 contents"> |
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+ <div class="page-header"> |
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+ <h1>best CV estimation</h1> |
|
| 58 |
+ <small class="dont-index">Source: <a href="https://github.com/Keniajin/protGear/blob/HEAD/R/cv_estimation_tag_functions.R" class="external-link"><code>R/cv_estimation_tag_functions.R</code></a></small> |
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+ <div class="hidden name"><code>best_CV_estimation.Rd</code></div> |
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+ </div> |
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+ |
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+ <div class="ref-description"> |
|
| 63 |
+ <p>A function to select the best CV by combining the replicates in |
|
| 64 |
+duplicates. The function has been build for up to to 3 replicates so far</p> |
|
| 65 |
+ </div> |
|
| 66 |
+ |
|
| 67 |
+ <div id="ref-usage"> |
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| 68 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">best_CV_estimation</span><span class="op">(</span><span class="va">dataCV</span>, <span class="va">slide_id</span>, <span class="va">lab_replicates</span>, <span class="va">cv_cut_off</span><span class="op">)</span></span></code></pre></div> |
|
| 69 |
+ </div> |
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| 70 |
+ |
|
| 71 |
+ <div id="arguments"> |
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| 72 |
+ <h2>Arguments</h2> |
|
| 73 |
+ <dl><dt>dataCV</dt> |
|
| 74 |
+<dd><p>A data frame</p></dd> |
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| 75 |
+ |
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+ |
|
| 77 |
+<dt>slide_id</dt> |
|
| 78 |
+<dd><p>A character string containing the identifier of the data |
|
| 79 |
+frame variable.</p></dd> |
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| 80 |
+ |
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| 81 |
+ |
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| 82 |
+<dt>lab_replicates</dt> |
|
| 83 |
+<dd><p>A numeric value indicating the |
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| 84 |
+number of lab replicates.</p></dd> |
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| 85 |
+ |
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| 86 |
+ |
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| 87 |
+<dt>cv_cut_off</dt> |
|
| 88 |
+<dd><p>a numeric value for the CV cut off. Should be between 0-100</p></dd> |
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| 89 |
+ |
|
| 90 |
+</dl></div> |
|
| 91 |
+ <div id="value"> |
|
| 92 |
+ <h2>Value</h2> |
|
| 93 |
+ |
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| 94 |
+ |
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| 95 |
+<p>A data frame with the best CV's estimated</p> |
|
| 96 |
+ </div> |
|
| 97 |
+ <div id="details"> |
|
| 98 |
+ <h2>Details</h2> |
|
| 99 |
+ <p>Select set of replicates with the best CV</p> |
|
| 100 |
+ </div> |
|
| 101 |
+ |
|
| 102 |
+ <div id="ref-examples"> |
|
| 103 |
+ <h2>Examples</h2> |
|
| 104 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">dataC</span> <span class="op"><-</span> <span class="fu">readr</span><span class="fu">::</span><span class="fu"><a href="https://readr.tidyverse.org/reference/read_delim.html" class="external-link">read_csv</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata"</span>,</span></span> |
|
| 105 |
+<span class="r-in"><span> <span class="st">"dataC.csv"</span>, package<span class="op">=</span><span class="st">"protGear"</span><span class="op">)</span><span class="op">)</span></span></span> |
|
| 106 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="font-weight: bold;">Rows: </span><span style="color: #0000BB;">567</span> <span style="font-weight: bold;">Columns: </span><span style="color: #0000BB;">11</span></span> |
|
| 107 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Column specification</span> <span style="color: #00BBBB;">────────────────────────────────────────────────────────</span></span> |
|
| 108 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="font-weight: bold;">Delimiter:</span> ","</span> |
|
| 109 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BB0000;">chr</span> (3): sampleID, antigen, iden</span> |
|
| 110 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">dbl</span> (8): sample_array_ID, FMedian, BGMedian, FMedianBG_correct, Block, Colum...</span> |
|
| 111 |
+<span class="r-msg co"><span class="r-pr">#></span> </span> |
|
| 112 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Use `spec()` to retrieve the full column specification for this data.</span> |
|
| 113 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Specify the column types or set `show_col_types = FALSE` to quiet this message.</span> |
|
| 114 |
+<span class="r-in"><span><span class="co">## this file has 3 lab replicates and the default names</span></span></span> |
|
| 115 |
+<span class="r-in"><span><span class="va">dataCV</span> <span class="op"><-</span> <span class="fu"><a href="cv_estimation.html">cv_estimation</a></span><span class="op">(</span><span class="va">dataC</span> ,lab_replicates<span class="op">=</span><span class="fl">3</span><span class="op">)</span></span></span> |
|
| 116 |
+<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>The replicates are as expected per sample per antigen</span> |
|
| 117 |
+<span class="r-in"><span><span class="fu">best_CV_estimation</span><span class="op">(</span><span class="va">dataCV</span>,slide_id <span class="op">=</span> <span class="st">"iden"</span>, lab_replicates <span class="op">=</span> <span class="fl">3</span>,</span></span> |
|
| 118 |
+<span class="r-in"><span> cv_cut_off <span class="op">=</span> <span class="fl">20</span><span class="op">)</span></span></span> |
|
| 119 |
+<span class="r-msg co"><span class="r-pr">#></span> Adding missing grouping variables: `row`</span> |
|
| 120 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 126 × 27</span></span> |
|
| 121 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: row [126]</span></span> |
|
| 122 |
+<span class="r-out co"><span class="r-pr">#></span> row antigen sampleID sample_ar…¹ meanX sdX sdX2_X3 sdX1_X3 sdX1_X2 CVX</span> |
|
| 123 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span> |
|
| 124 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 1 AMA1 0.0085 11 643. 98.5 70 69.3 139. 15.3 </span> |
|
| 125 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2 AMA1 0.0255 8 699 52.6 74.2 33.9 40.3 7.52</span> |
|
| 126 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 3 AMA1 0.076 5 633. 81.3 35.4 77.1 112. 12.8 </span> |
|
| 127 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 4 AMA1 0.23 2 <span style="text-decoration: underline;">1</span>725. 60.5 32.5 84.8 52.3 3.51</span> |
|
| 128 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 5 AMA1 0.73 19 <span style="text-decoration: underline;">2</span>504. 119. 166. 61.5 105. 4.75</span> |
|
| 129 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 6 AMA1 177.78 4 <span style="text-decoration: underline;">58</span>262 709. 994. 383. 612. 1.22</span> |
|
| 130 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 7 AMA1 19.75 10 <span style="text-decoration: underline;">64</span>143. 353. 476. 367. 109. 0.55</span> |
|
| 131 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 8 AMA1 2.19 16 <span style="text-decoration: underline;">9</span>243 383. 528. 156. 372. 4.15</span> |
|
| 132 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 9 AMA1 533 1 <span style="text-decoration: underline;">53</span>180. 559. 117. 735. 619. 1.05</span> |
|
| 133 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 10 AMA1 59.26 7 <span style="text-decoration: underline;">61</span>601 894. <span style="text-decoration: underline;">1</span>078. <span style="text-decoration: underline;">1</span>111. 32.5 1.45</span> |
|
| 134 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 116 more rows, 17 more variables: CVX2_X3 <dbl>, CVX1_X3 <dbl>,</span></span> |
|
| 135 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CVX1_X2 <dbl>, cvCat_all <chr>, cvSelected_all <dbl>, iden <chr>,</span></span> |
|
| 136 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># `1` <dbl>, `2` <dbl>, `3` <dbl>, x <chr>, meanX1_X2 <dbl>, meanX1_X3 <dbl>,</span></span> |
|
| 137 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># meanX2_X3 <dbl>, meanSelected <dbl>, mean_best_CV <dbl>, best_CV <dbl>,</span></span> |
|
| 138 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># best_CV_cat <chr>, and abbreviated variable name ¹sample_array_ID</span></span> |
|
| 139 |
+</code></pre></div> |
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+ <a class="navbar-link" href="../index.html">protGear</a> |
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+ <div id="navbar" class="navbar-collapse collapse"> |
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+<li> |
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+ <a href="../news/index.html">Changelog</a> |
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+</li> |
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+ </ul><ul class="nav navbar-nav navbar-right"><li> |
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+ <a href="https://github.com/Keniajin/protGear/" class="external-link"> |
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+ <span class="fab fa-github fa-lg"></span> |
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+ |
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+ </a> |
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+</li> |
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+ </ul></div><!--/.nav-collapse --> |
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+ </div><!--/.container --> |
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+</div><!--/.navbar --> |
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+ |
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+ |
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+ |
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+ </header><div class="row"> |
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+ <div class="col-md-9 contents"> |
|
| 55 |
+ <div class="page-header"> |
|
| 56 |
+ <h1>bg_correct</h1> |
|
| 57 |
+ <small class="dont-index">Source: <a href="https://github.com/Keniajin/protGear/blob/HEAD/R/read_files_functions.R" class="external-link"><code>R/read_files_functions.R</code></a></small> |
|
| 58 |
+ <div class="hidden name"><code>bg_correct.Rd</code></div> |
|
| 59 |
+ </div> |
|
| 60 |
+ |
|
| 61 |
+ <div class="ref-description"> |
|
| 62 |
+ <p>A generic function to perform background correction.</p> |
|
| 63 |
+ </div> |
|
| 64 |
+ |
|
| 65 |
+ <div id="ref-usage"> |
|
| 66 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">bg_correct</span><span class="op">(</span><span class="va">iden</span>, <span class="va">Data1</span>, <span class="va">genepix_vars</span>, method <span class="op">=</span> <span class="st">"subtract_local"</span><span class="op">)</span></span></code></pre></div> |
|
| 67 |
+ </div> |
|
| 68 |
+ |
|
| 69 |
+ <div id="arguments"> |
|
| 70 |
+ <h2>Arguments</h2> |
|
| 71 |
+ <dl><dt>iden</dt> |
|
| 72 |
+<dd><p>A character indicating the name of the object to be |
|
| 73 |
+used under Data1</p></dd> |
|
| 74 |
+ |
|
| 75 |
+ |
|
| 76 |
+<dt>Data1</dt> |
|
| 77 |
+<dd><p>A data frame with sample identifiers merged with micro |
|
| 78 |
+array data.</p></dd> |
|
| 79 |
+ |
|
| 80 |
+ |
|
| 81 |
+<dt>genepix_vars</dt> |
|
| 82 |
+<dd><p>A list of specific definitions of the experiment design. |
|
| 83 |
+See <code><a href="array_vars.html">array_vars</a></code>.</p></dd> |
|
| 84 |
+ |
|
| 85 |
+ |
|
| 86 |
+<dt>method</dt> |
|
| 87 |
+<dd><p>a description of the background correction to be used. |
|
| 88 |
+ Possible values are <code>"none","subtract_local", |
|
| 89 |
+"subtract_global","movingmin_bg","minimum_half","edwards" or "normexp"</code>. |
|
| 90 |
+The default is <code>"subtract_local"</code>.</p></dd> |
|
| 91 |
+ |
|
| 92 |
+</dl></div> |
|
| 93 |
+ <div id="value"> |
|
| 94 |
+ <h2>Value</h2> |
|
| 95 |
+ |
|
| 96 |
+ |
|
| 97 |
+<p>A data frame with background corrected data</p> |
|
| 98 |
+ </div> |
|
| 99 |
+ <div id="details"> |
|
| 100 |
+ <h2>Details</h2> |
|
| 101 |
+ <p>Background correction</p> |
|
| 102 |
+<p>The function implements background correction methods developed |
|
| 103 |
+by <code><a href="https://rdrr.io/pkg/limma/man/backgroundcorrect.html" class="external-link">backgroundCorrect</a></code>. But the |
|
| 104 |
+<code>minimum_half and movingmin_bg</code> uses the block of the protein array as |
|
| 105 |
+the grid. If method="movingmin_bg" the minimum |
|
| 106 |
+background value within a block is subtracted. |
|
| 107 |
+If method="minimum_half" then any intensity which is negative after |
|
| 108 |
+background subtraction is reset to be equal to half the |
|
| 109 |
+minimum positive value in |
|
| 110 |
+a block. If method="movingmin_value" then any intensity which is negative |
|
| 111 |
+after background subtraction is reset to the minimum positive value |
|
| 112 |
+in a block. For <code>edwards</code> we implement a similar algorithm with |
|
| 113 |
+<code>limma::backgroundCorrect(method="edwards")</code> and for <code>'normexp'</code> |
|
| 114 |
+we use the saddle-point approximation to maximum likelihood, |
|
| 115 |
+<code><a href="https://rdrr.io/pkg/limma/man/backgroundcorrect.html" class="external-link">backgroundCorrect</a></code> for more details.</p> |
|
| 116 |
+ </div> |
|
| 117 |
+ |
|
| 118 |
+ </div> |
|
| 119 |
+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |
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| 120 |
+ <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> |
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| 121 |
+ </nav></div> |
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+</div> |
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+ |
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+ |
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+ <footer><div class="copyright"> |
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+ <p></p><p>Developed by Kennedy Mwai, James Mburu.</p> |
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+ |
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| 129 |
+<div class="pkgdown"> |
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+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> |
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Extract buffer spots of data — buffer_spots • protGear</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Extract buffer spots of data — buffer_spots"><meta property="og:description" content="A function to extract the buffer spots data. A buffer spot only |
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| 3 |
+ has the solution for |
|
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+ proprietary ingredients for stabilizing protein and minimizing evaporation."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> |
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+ <div class="container template-reference-topic"> |
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+<li class="dropdown"> |
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+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> |
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+ |
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+ </a> |
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+ <ul class="dropdown-menu" role="menu"><li> |
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+ <a href="../articles/vignette.html">protGear vignette processing suite</a> |
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+ </li> |
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+ </ul></li> |
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+<li> |
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+ <a href="../news/index.html">Changelog</a> |
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+</li> |
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+ </ul><ul class="nav navbar-nav navbar-right"><li> |
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+ <a href="https://github.com/Keniajin/protGear/" class="external-link"> |
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+ <span class="fab fa-github fa-lg"></span> |
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+ |
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+ </a> |
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+</li> |
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+ </ul></div><!--/.nav-collapse --> |
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+ </div><!--/.container --> |
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+</div><!--/.navbar --> |
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+ |
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+ |
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+ |
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+ </header><div class="row"> |
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+ <div class="col-md-9 contents"> |
|
| 57 |
+ <div class="page-header"> |
|
| 58 |
+ <h1>Extract buffer spots of data</h1> |
|
| 59 |
+ <small class="dont-index">Source: <a href="https://github.com/Keniajin/protGear/blob/HEAD/R/buffer_spot_functions.R" class="external-link"><code>R/buffer_spot_functions.R</code></a></small> |
|
| 60 |
+ <div class="hidden name"><code>buffer_spots.Rd</code></div> |
|
| 61 |
+ </div> |
|
| 62 |
+ |
|
| 63 |
+ <div class="ref-description"> |
|
| 64 |
+ <p>A function to extract the buffer spots data. A buffer spot only |
|
| 65 |
+ has the solution for |
|
| 66 |
+ proprietary ingredients for stabilizing protein and minimizing evaporation.</p> |
|
| 67 |
+ </div> |
|
| 68 |
+ |
|
| 69 |
+ <div id="ref-usage"> |
|
| 70 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">buffer_spots</span><span class="op">(</span><span class="va">Data1</span>, buffer_spot <span class="op">=</span> <span class="st">"buffer"</span><span class="op">)</span></span></code></pre></div> |
|
| 71 |
+ </div> |
|
| 72 |
+ |
|
| 73 |
+ <div id="arguments"> |
|
| 74 |
+ <h2>Arguments</h2> |
|
| 75 |
+ <dl><dt>Data1</dt> |
|
| 76 |
+<dd><p>An object of the class data frame</p></dd> |
|
| 77 |
+ |
|
| 78 |
+ |
|
| 79 |
+<dt>buffer_spot</dt> |
|
| 80 |
+<dd><p>A character string containing the name of the buffer |
|
| 81 |
+spots.</p></dd> |
|
| 82 |
+ |
|
| 83 |
+</dl></div> |
|
| 84 |
+ <div id="value"> |
|
| 85 |
+ <h2>Value</h2> |
|
| 86 |
+ |
|
| 87 |
+ |
|
| 88 |
+<p>A data frame of the buffer control spots</p> |
|
| 89 |
+ </div> |
|
| 90 |
+ |
|
| 91 |
+ <div id="ref-examples"> |
|
| 92 |
+ <h2>Examples</h2> |
|
| 93 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">bg_correct_df</span> <span class="op"><-</span> <span class="fu">readr</span><span class="fu">::</span><span class="fu"><a href="https://readr.tidyverse.org/reference/read_delim.html" class="external-link">read_csv</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata"</span>, <span class="st">"Data1_sample.csv"</span>,</span></span> |
|
| 94 |
+<span class="r-in"><span>package<span class="op">=</span><span class="st">"protGear"</span><span class="op">)</span><span class="op">)</span></span></span> |
|
| 95 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="font-weight: bold;">Rows: </span><span style="color: #0000BB;">378</span> <span style="font-weight: bold;">Columns: </span><span style="color: #0000BB;">11</span></span> |
|
| 96 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Column specification</span> <span style="color: #00BBBB;">────────────────────────────────────────────────────────</span></span> |
|
| 97 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="font-weight: bold;">Delimiter:</span> ","</span> |
|
| 98 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BB0000;">chr</span> (3): sampleID, antigen, iden</span> |
|
| 99 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">dbl</span> (8): sample_array_ID, FMedian, BGMedian, FMedianBG_correct, Block, Colum...</span> |
|
| 100 |
+<span class="r-msg co"><span class="r-pr">#></span> </span> |
|
| 101 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Use `spec()` to retrieve the full column specification for this data.</span> |
|
| 102 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Specify the column types or set `show_col_types = FALSE` to quiet this message.</span> |
|
| 103 |
+<span class="r-in"><span><span class="fu">buffer_spots</span><span class="op">(</span>Data1 <span class="op">=</span> <span class="va">bg_correct_df</span><span class="op">)</span></span></span> |
|
| 104 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 0 × 6</span></span> |
|
| 105 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 6 variables: sampleID <chr>, antigen <chr>, FMedianBG_correct <dbl>,</span></span> |
|
| 106 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Block <dbl>, Column <dbl>, Row <dbl></span></span> |
|
| 107 |
+</code></pre></div> |
|
| 108 |
+ </div> |
|
| 109 |
+ </div> |
|
| 110 |
+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |
|
| 111 |
+ <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> |
|
| 112 |
+ </nav></div> |
|
| 113 |
+</div> |
|
| 114 |
+ |
|
| 115 |
+ |
|
| 116 |
+ <footer><div class="copyright"> |
|
| 117 |
+ <p></p><p>Developed by Kennedy Mwai, James Mburu.</p> |
|
| 118 |
+</div> |
|
| 119 |
+ |
|
| 120 |
+<div class="pkgdown"> |
|
| 121 |
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> |
|
| 122 |
+</div> |
|
| 123 |
+ |
|
| 124 |
+ </footer></div> |
|
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+ |
|
| 126 |
+ |
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| 127 |
+ |
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+ |
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| 129 |
+ |
|
| 130 |
+ |
|
| 131 |
+ </body></html> |
|
| 132 |
+ |
| 0 | 133 |
new file mode 100644 |
| ... | ... |
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| 1 |
+<!DOCTYPE html> |
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>\\_End_Function_\\ # |
|
| 3 |
+Check existing sample ID names — check_sampleID_files • protGear</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="\\_End_Function_\\ # |
|
| 4 |
+Check existing sample ID names — check_sampleID_files"><meta property="og:description" content="A generic function to check if the file(s) |
|
| 5 |
+with the MFI values have a corresponding sample ID file. Sample ID file is |
|
| 6 |
+a file with the identifiers for the samples in array file."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> |
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+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> |
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+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> |
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+<![endif]--></head><body data-spy="scroll" data-target="#toc"> |
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+ <span class="navbar-brand"> |
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+ <a class="navbar-link" href="../index.html">protGear</a> |
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+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.2.1</span> |
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+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> |
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+ Articles |
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+ |
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+ <span class="caret"></span> |
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+ </a> |
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+ <ul class="dropdown-menu" role="menu"><li> |
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+ <a href="../articles/vignette.html">protGear vignette processing suite</a> |
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+ </li> |
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+ </ul></li> |
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+<li> |
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+ <a href="../news/index.html">Changelog</a> |
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+</li> |
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+ </ul><ul class="nav navbar-nav navbar-right"><li> |
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+ <a href="https://github.com/Keniajin/protGear/" class="external-link"> |
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+ <span class="fab fa-github fa-lg"></span> |
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+ |
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+ </a> |
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+</li> |
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+ </ul></div><!--/.nav-collapse --> |
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+ </div><!--/.container --> |
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+</div><!--/.navbar --> |
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+ |
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+ |
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+ |
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| 57 |
+ </header><div class="row"> |
|
| 58 |
+ <div class="col-md-9 contents"> |
|
| 59 |
+ <div class="page-header"> |
|
| 60 |
+ <h1>\\_End_Function_\\ # |
|
| 61 |
+Check existing sample ID names</h1> |
|
| 62 |
+ <small class="dont-index">Source: <a href="https://github.com/Keniajin/protGear/blob/HEAD/R/global_functions.R" class="external-link"><code>R/global_functions.R</code></a></small> |
|
| 63 |
+ <div class="hidden name"><code>check_sampleID_files.Rd</code></div> |
|
| 64 |
+ </div> |
|
| 65 |
+ |
|
| 66 |
+ <div class="ref-description"> |
|
| 67 |
+ <p>A generic function to check if the file(s) |
|
| 68 |
+with the MFI values have a corresponding sample ID file. Sample ID file is |
|
| 69 |
+a file with the identifiers for the samples in array file.</p> |
|
| 70 |
+ </div> |
|
| 71 |
+ |
|
| 72 |
+ <div id="ref-usage"> |
|
| 73 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">check_sampleID_files</span><span class="op">(</span><span class="va">genepix_vars</span><span class="op">)</span></span></code></pre></div> |
|
| 74 |
+ </div> |
|
| 75 |
+ |
|
| 76 |
+ <div id="arguments"> |
|
| 77 |
+ <h2>Arguments</h2> |
|
| 78 |
+ <dl><dt>genepix_vars</dt> |
|
| 79 |
+<dd><p>A list of specific definitions of the experiment design. |
|
| 80 |
+See <code><a href="array_vars.html">array_vars</a></code>.</p></dd> |
|
| 81 |
+ |
|
| 82 |
+</dl></div> |
|
| 83 |
+ <div id="value"> |
|
| 84 |
+ <h2>Value</h2> |
|
| 85 |
+ |
|
| 86 |
+ |
|
| 87 |
+<p>A file with missing corresponding sample ID files</p> |
|
| 88 |
+ </div> |
|
| 89 |
+ |
|
| 90 |
+ <div id="ref-examples"> |
|
| 91 |
+ <h2>Examples</h2> |
|
| 92 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">genepix_vars</span> <span class="op"><-</span> <span class="fu"><a href="array_vars.html">array_vars</a></span><span class="op">(</span></span></span> |
|
| 93 |
+<span class="r-in"><span>channel <span class="op">=</span> <span class="st">"635"</span>,</span></span> |
|
| 94 |
+<span class="r-in"><span>chip_path <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata"</span>, <span class="st">"array_data/machine1/"</span>, </span></span> |
|
| 95 |
+<span class="r-in"><span>package<span class="op">=</span><span class="st">"protGear"</span><span class="op">)</span>,</span></span> |
|
| 96 |
+<span class="r-in"><span>totsamples <span class="op">=</span> <span class="fl">21</span>,</span></span> |
|
| 97 |
+<span class="r-in"><span>blockspersample <span class="op">=</span> <span class="fl">2</span>,</span></span> |
|
| 98 |
+<span class="r-in"><span>mig_prefix <span class="op">=</span> <span class="st">"_first"</span>,</span></span> |
|
| 99 |
+<span class="r-in"><span>machine <span class="op">=</span> <span class="fl">1</span>,</span></span> |
|
| 100 |
+<span class="r-in"><span>date_process <span class="op">=</span> <span class="st">"0520"</span></span></span> |
|
| 101 |
+<span class="r-in"><span><span class="op">)</span></span></span> |
|
| 102 |
+<span class="r-in"><span><span class="fu">check_sampleID_files</span><span class="op">(</span><span class="va">genepix_vars</span><span class="op">)</span></span></span> |
|
| 103 |
+<span class="r-out co"><span class="r-pr">#></span> [1] "BRB001" "KK2-06"</span> |
|
| 104 |
+</code></pre></div> |
|
| 105 |
+ </div> |
|
| 106 |
+ </div> |
|
| 107 |
+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |
|
| 108 |
+ <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> |
|
| 109 |
+ </nav></div> |
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+</div> |
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| 111 |
+ |
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+ |
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| 113 |
+ <footer><div class="copyright"> |
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| 114 |
+ <p></p><p>Developed by Kennedy Mwai, James Mburu.</p> |
|
| 115 |
+</div> |
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| 116 |
+ |
|
| 117 |
+<div class="pkgdown"> |
|
| 118 |
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> |
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+</div> |
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+ |
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+ </footer></div> |
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+ |
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+ |
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+ |
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+ |
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+ |
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+ |
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| 128 |
+ </body></html> |
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| 129 |
+ |
| 0 | 130 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,111 @@ |
| 1 |
+<!DOCTYPE html> |
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| 2 |
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Title Create directory function — create_dir • protGear</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Title Create directory function — create_dir"><meta property="og:description" content="creating a directory"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> |
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+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> |
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+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> |
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+<![endif]--></head><body data-spy="scroll" data-target="#toc"> |
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+ |
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+ |
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+ <div class="container template-reference-topic"> |
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+ <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> |
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+ <div class="navbar-header"> |
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+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> |
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+ <span class="sr-only">Toggle navigation</span> |
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+ <span class="icon-bar"></span> |
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+ <span class="icon-bar"></span> |
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+ <span class="icon-bar"></span> |
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+ </button> |
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+ <span class="navbar-brand"> |
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+ <a class="navbar-link" href="../index.html">protGear</a> |
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+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.2.1</span> |
|
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+ </span> |
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+ </div> |
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+ |
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+ <div id="navbar" class="navbar-collapse collapse"> |
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+ <ul class="nav navbar-nav"><li> |
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+ <a href="../reference/index.html">Reference</a> |
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+</li> |
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+<li class="dropdown"> |
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+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> |
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+ Articles |
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+ |
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+ <span class="caret"></span> |
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+ </a> |
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+ <ul class="dropdown-menu" role="menu"><li> |
|
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+ <a href="../articles/vignette.html">protGear vignette processing suite</a> |
|
| 36 |
+ </li> |
|
| 37 |
+ </ul></li> |
|
| 38 |
+<li> |
|
| 39 |
+ <a href="../news/index.html">Changelog</a> |
|
| 40 |
+</li> |
|
| 41 |
+ </ul><ul class="nav navbar-nav navbar-right"><li> |
|
| 42 |
+ <a href="https://github.com/Keniajin/protGear/" class="external-link"> |
|
| 43 |
+ <span class="fab fa-github fa-lg"></span> |
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+ |
|
| 45 |
+ </a> |
|
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+</li> |
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+ </ul></div><!--/.nav-collapse --> |
|
| 48 |
+ </div><!--/.container --> |
|
| 49 |
+</div><!--/.navbar --> |
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+ |
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| 51 |
+ |
|
| 52 |
+ |
|
| 53 |
+ </header><div class="row"> |
|
| 54 |
+ <div class="col-md-9 contents"> |
|
| 55 |
+ <div class="page-header"> |
|
| 56 |
+ <h1>Title Create directory function</h1> |
|
| 57 |
+ <small class="dont-index">Source: <a href="https://github.com/Keniajin/protGear/blob/HEAD/R/global_functions.R" class="external-link"><code>R/global_functions.R</code></a></small> |
|
| 58 |
+ <div class="hidden name"><code>create_dir.Rd</code></div> |
|
| 59 |
+ </div> |
|
| 60 |
+ |
|
| 61 |
+ <div class="ref-description"> |
|
| 62 |
+ <p>creating a directory</p> |
|
| 63 |
+ </div> |
|
| 64 |
+ |
|
| 65 |
+ <div id="ref-usage"> |
|
| 66 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">create_dir</span><span class="op">(</span><span class="va">path</span><span class="op">)</span></span></code></pre></div> |
|
| 67 |
+ </div> |
|
| 68 |
+ |
|
| 69 |
+ <div id="arguments"> |
|
| 70 |
+ <h2>Arguments</h2> |
|
| 71 |
+ <dl><dt>path</dt> |
|
| 72 |
+<dd><p>folder location to create a directory</p></dd> |
|
| 73 |
+ |
|
| 74 |
+</dl></div> |
|
| 75 |
+ <div id="value"> |
|
| 76 |
+ <h2>Value</h2> |
|
| 77 |
+ |
|
| 78 |
+ |
|
| 79 |
+<p>created directory</p> |
|
| 80 |
+ </div> |
|
| 81 |
+ |
|
| 82 |
+ <div id="ref-examples"> |
|
| 83 |
+ <h2>Examples</h2> |
|
| 84 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">create_dir</span><span class="op">(</span><span class="st">"data/sample_folder"</span><span class="op">)</span></span></span> |
|
| 85 |
+<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>cannot create dir 'data\sample_folder', reason 'No such file or directory'</span> |
|
| 86 |
+</code></pre></div> |
|
| 87 |
+ </div> |
|
| 88 |
+ </div> |
|
| 89 |
+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |
|
| 90 |
+ <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> |
|
| 91 |
+ </nav></div> |
|
| 92 |
+</div> |
|
| 93 |
+ |
|
| 94 |
+ |
|
| 95 |
+ <footer><div class="copyright"> |
|
| 96 |
+ <p></p><p>Developed by Kennedy Mwai, James Mburu.</p> |
|
| 97 |
+</div> |
|
| 98 |
+ |
|
| 99 |
+<div class="pkgdown"> |
|
| 100 |
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> |
|
| 101 |
+</div> |
|
| 102 |
+ |
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+ </footer></div> |
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+ |
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+ |
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+ |
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+ |
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| 108 |
+ |
|
| 109 |
+ |
|
| 110 |
+ </body></html> |
|
| 111 |
+ |
| 0 | 112 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,165 @@ |
| 1 |
+<!DOCTYPE html> |
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+ <div class="col-md-9 contents"> |
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+ <div class="page-header"> |
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+ <h1>cv by sample</h1> |
|
| 58 |
+ <small class="dont-index">Source: <a href="https://github.com/Keniajin/protGear/blob/HEAD/R/cv_by_sample_estimation.R" class="external-link"><code>R/cv_by_sample_estimation.R</code></a></small> |
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+ <div class="hidden name"><code>cv_by_sample_estimation.Rd</code></div> |
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+ </div> |
|
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+ |
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+ <div class="ref-description"> |
|
| 63 |
+ <p>A function to give the summary of |
|
| 64 |
+the CV's by the sampleID</p> |
|
| 65 |
+ </div> |
|
| 66 |
+ |
|
| 67 |
+ <div id="ref-usage"> |
|
| 68 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">cv_by_sample_estimation</span><span class="op">(</span></span> |
|
| 69 |
+<span> <span class="va">dataCV</span>,</span> |
|
| 70 |
+<span> <span class="va">cv_variable</span>,</span> |
|
| 71 |
+<span> <span class="va">lab_replicates</span>,</span> |
|
| 72 |
+<span> sampleID_var <span class="op">=</span> <span class="st">"sampleID"</span></span> |
|
| 73 |
+<span><span class="op">)</span></span></code></pre></div> |
|
| 74 |
+ </div> |
|
| 75 |
+ |
|
| 76 |
+ <div id="arguments"> |
|
| 77 |
+ <h2>Arguments</h2> |
|
| 78 |
+ <dl><dt>dataCV</dt> |
|
| 79 |
+<dd><p>A dataframe</p></dd> |
|
| 80 |
+ |
|
| 81 |
+ |
|
| 82 |
+<dt>cv_variable</dt> |
|
| 83 |
+<dd><p>A character string containing the identifier |
|
| 84 |
+of the variable with CV values.</p></dd> |
|
| 85 |
+ |
|
| 86 |
+ |
|
| 87 |
+<dt>lab_replicates</dt> |
|
| 88 |
+<dd><p>A numeric value indicating the number of lab |
|
| 89 |
+replicates.</p></dd> |
|
| 90 |
+ |
|
| 91 |
+ |
|
| 92 |
+<dt>sampleID_var</dt> |
|
| 93 |
+<dd><p>A character string containing the name of the |
|
| 94 |
+sample identifier variable. Default set to 'sampleID'</p></dd> |
|
| 95 |
+ |
|
| 96 |
+</dl></div> |
|
| 97 |
+ <div id="value"> |
|
| 98 |
+ <h2>Value</h2> |
|
| 99 |
+ |
|
| 100 |
+ |
|
| 101 |
+<p>A data frame of CV calculated by sample</p> |
|
| 102 |
+ </div> |
|
| 103 |
+ <div id="details"> |
|
| 104 |
+ <h2>Details</h2> |
|
| 105 |
+ <p>Summarise CV by samples</p> |
|
| 106 |
+ </div> |
|
| 107 |
+ |
|
| 108 |
+ <div id="ref-examples"> |
|
| 109 |
+ <h2>Examples</h2> |
|
| 110 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">dataC</span> <span class="op"><-</span> <span class="fu">readr</span><span class="fu">::</span><span class="fu"><a href="https://readr.tidyverse.org/reference/read_delim.html" class="external-link">read_csv</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata"</span>, </span></span> |
|
| 111 |
+<span class="r-in"><span><span class="st">"dataC.csv"</span>, package<span class="op">=</span><span class="st">"protGear"</span><span class="op">)</span><span class="op">)</span></span></span> |
|
| 112 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="font-weight: bold;">Rows: </span><span style="color: #0000BB;">567</span> <span style="font-weight: bold;">Columns: </span><span style="color: #0000BB;">11</span></span> |
|
| 113 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Column specification</span> <span style="color: #00BBBB;">────────────────────────────────────────────────────────</span></span> |
|
| 114 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="font-weight: bold;">Delimiter:</span> ","</span> |
|
| 115 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BB0000;">chr</span> (3): sampleID, antigen, iden</span> |
|
| 116 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">dbl</span> (8): sample_array_ID, FMedian, BGMedian, FMedianBG_correct, Block, Colum...</span> |
|
| 117 |
+<span class="r-msg co"><span class="r-pr">#></span> </span> |
|
| 118 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Use `spec()` to retrieve the full column specification for this data.</span> |
|
| 119 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Specify the column types or set `show_col_types = FALSE` to quiet this message.</span> |
|
| 120 |
+<span class="r-in"><span><span class="co">## this file has 3 lab replicates and the default names</span></span></span> |
|
| 121 |
+<span class="r-in"><span><span class="va">dataCV</span> <span class="op"><-</span> <span class="fu"><a href="cv_estimation.html">cv_estimation</a></span><span class="op">(</span><span class="va">dataC</span> ,lab_replicates<span class="op">=</span><span class="fl">3</span><span class="op">)</span></span></span> |
|
| 122 |
+<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>The replicates are as expected per sample per antigen</span> |
|
| 123 |
+<span class="r-in"><span><span class="fu">cv_by_sample_estimation</span><span class="op">(</span><span class="va">dataCV</span>, cv_variable <span class="op">=</span> <span class="st">"cvCat_all"</span>,</span></span> |
|
| 124 |
+<span class="r-in"><span> lab_replicates <span class="op">=</span> <span class="fl">3</span><span class="op">)</span></span></span> |
|
| 125 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 21 × 7</span></span> |
|
| 126 |
+<span class="r-out co"><span class="r-pr">#></span> sampleID `CV <= 20_n` `CV <= 20_perc` `CV > 20_n` CV > 20_p…¹ Other…² Other…³</span> |
|
| 127 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span> |
|
| 128 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 0.0085 5 83.3 1 16.7 0 0 </span> |
|
| 129 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 0.0255 3 50 2 33.3 1 16.7</span> |
|
| 130 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 0.076 3 50 2 33.3 1 16.7</span> |
|
| 131 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 0.23 4 66.7 2 33.3 0 0 </span> |
|
| 132 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 0.73 4 66.7 1 16.7 1 16.7</span> |
|
| 133 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 177.78 6 100 0 0 0 0 </span> |
|
| 134 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 19.75 5 83.3 1 16.7 0 0 </span> |
|
| 135 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2.19 3 50 3 50 0 0 </span> |
|
| 136 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 533 6 100 0 0 0 0 </span> |
|
| 137 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 59.26 5 83.3 1 16.7 0 0 </span> |
|
| 138 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 11 more rows, and abbreviated variable names ¹`CV > 20_perc`,</span></span> |
|
| 139 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ²Others_n, ³Others_perc</span></span> |
|
| 140 |
+</code></pre></div> |
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| 40 |
+ <a href="../news/index.html">Changelog</a> |
|
| 41 |
+</li> |
|
| 42 |
+ </ul><ul class="nav navbar-nav navbar-right"><li> |
|
| 43 |
+ <a href="https://github.com/Keniajin/protGear/" class="external-link"> |
|
| 44 |
+ <span class="fab fa-github fa-lg"></span> |
|
| 45 |
+ |
|
| 46 |
+ </a> |
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| 47 |
+</li> |
|
| 48 |
+ </ul></div><!--/.nav-collapse --> |
|
| 49 |
+ </div><!--/.container --> |
|
| 50 |
+</div><!--/.navbar --> |
|
| 51 |
+ |
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| 52 |
+ |
|
| 53 |
+ |
|
| 54 |
+ </header><div class="row"> |
|
| 55 |
+ <div class="col-md-9 contents"> |
|
| 56 |
+ <div class="page-header"> |
|
| 57 |
+ <h1>cv_estimation</h1> |
|
| 58 |
+ <small class="dont-index">Source: <a href="https://github.com/Keniajin/protGear/blob/HEAD/R/cv_estimation_tag_functions.R" class="external-link"><code>R/cv_estimation_tag_functions.R</code></a></small> |
|
| 59 |
+ <div class="hidden name"><code>cv_estimation.Rd</code></div> |
|
| 60 |
+ </div> |
|
| 61 |
+ |
|
| 62 |
+ <div class="ref-description"> |
|
| 63 |
+ <p>A function to calculate the CV for the technical lab replicates. |
|
| 64 |
+ The default values are set as per the object names generated by machine</p> |
|
| 65 |
+ </div> |
|
| 66 |
+ |
|
| 67 |
+ <div id="ref-usage"> |
|
| 68 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">cv_estimation</span><span class="op">(</span></span> |
|
| 69 |
+<span> <span class="va">dataC</span>,</span> |
|
| 70 |
+<span> <span class="va">lab_replicates</span>,</span> |
|
| 71 |
+<span> sampleID_var <span class="op">=</span> <span class="st">"sampleID"</span>,</span> |
|
| 72 |
+<span> antigen_var <span class="op">=</span> <span class="st">"antigen"</span>,</span> |
|
| 73 |
+<span> replicate_var <span class="op">=</span> <span class="st">"replicate"</span>,</span> |
|
| 74 |
+<span> mfi_var <span class="op">=</span> <span class="st">"FMedianBG_correct"</span>,</span> |
|
| 75 |
+<span> cv_cut_off <span class="op">=</span> <span class="fl">20</span></span> |
|
| 76 |
+<span><span class="op">)</span></span></code></pre></div> |
|
| 77 |
+ </div> |
|
| 78 |
+ |
|
| 79 |
+ <div id="arguments"> |
|
| 80 |
+ <h2>Arguments</h2> |
|
| 81 |
+ <dl><dt>dataC</dt> |
|
| 82 |
+<dd><p>A dataset a data frame with feature variables to be used</p></dd> |
|
| 83 |
+ |
|
| 84 |
+ |
|
| 85 |
+<dt>lab_replicates</dt> |
|
| 86 |
+<dd><p>A numeric value indicating the number of lab replicates</p></dd> |
|
| 87 |
+ |
|
| 88 |
+ |
|
| 89 |
+<dt>sampleID_var</dt> |
|
| 90 |
+<dd><p>A character string containing the name of the sample |
|
| 91 |
+identifier variable. Default set to 'sampleID'</p></dd> |
|
| 92 |
+ |
|
| 93 |
+ |
|
| 94 |
+<dt>antigen_var</dt> |
|
| 95 |
+<dd><p>A character string containing the name of the |
|
| 96 |
+features/protein variable. Default to 'antigen'</p></dd> |
|
| 97 |
+ |
|
| 98 |
+ |
|
| 99 |
+<dt>replicate_var</dt> |
|
| 100 |
+<dd><p>A character string containing the name of the replicate |
|
| 101 |
+variable. Default to 'replicate'</p></dd> |
|
| 102 |
+ |
|
| 103 |
+ |
|
| 104 |
+<dt>mfi_var</dt> |
|
| 105 |
+<dd><p>A character string containing the name of the variable with |
|
| 106 |
+MFI value.Assuming background correction is done already. |
|
| 107 |
+Default to 'FMedianBG_correct'</p></dd> |
|
| 108 |
+ |
|
| 109 |
+ |
|
| 110 |
+<dt>cv_cut_off</dt> |
|
| 111 |
+<dd><p>Optional value indicating the cut off of flagging CV's. |
|
| 112 |
+Default set at 20.</p></dd> |
|
| 113 |
+ |
|
| 114 |
+</dl></div> |
|
| 115 |
+ <div id="value"> |
|
| 116 |
+ <h2>Value</h2> |
|
| 117 |
+ |
|
| 118 |
+ |
|
| 119 |
+<p>A data frame where CV's of the replicates have been calculated</p> |
|
| 120 |
+ </div> |
|
| 121 |
+ <div id="details"> |
|
| 122 |
+ <h2>Details</h2> |
|
| 123 |
+ <p>Coefficient of Variation</p> |
|
| 124 |
+ </div> |
|
| 125 |
+ |
|
| 126 |
+ <div id="ref-examples"> |
|
| 127 |
+ <h2>Examples</h2> |
|
| 128 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">dataC</span> <span class="op"><-</span> <span class="fu">readr</span><span class="fu">::</span><span class="fu"><a href="https://readr.tidyverse.org/reference/read_delim.html" class="external-link">read_csv</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata"</span>, </span></span> |
|
| 129 |
+<span class="r-in"><span><span class="st">"dataC.csv"</span>, package<span class="op">=</span><span class="st">"protGear"</span><span class="op">)</span><span class="op">)</span></span></span> |
|
| 130 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="font-weight: bold;">Rows: </span><span style="color: #0000BB;">567</span> <span style="font-weight: bold;">Columns: </span><span style="color: #0000BB;">11</span></span> |
|
| 131 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Column specification</span> <span style="color: #00BBBB;">────────────────────────────────────────────────────────</span></span> |
|
| 132 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="font-weight: bold;">Delimiter:</span> ","</span> |
|
| 133 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BB0000;">chr</span> (3): sampleID, antigen, iden</span> |
|
| 134 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">dbl</span> (8): sample_array_ID, FMedian, BGMedian, FMedianBG_correct, Block, Colum...</span> |
|
| 135 |
+<span class="r-msg co"><span class="r-pr">#></span> </span> |
|
| 136 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Use `spec()` to retrieve the full column specification for this data.</span> |
|
| 137 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Specify the column types or set `show_col_types = FALSE` to quiet this message.</span> |
|
| 138 |
+<span class="r-in"><span><span class="co">## this file has 3 lab replicates and the default names</span></span></span> |
|
| 139 |
+<span class="r-in"><span><span class="fu">cv_estimation</span><span class="op">(</span><span class="va">dataC</span> ,lab_replicates<span class="op">=</span><span class="fl">3</span><span class="op">)</span></span></span> |
|
| 140 |
+<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>The replicates are as expected per sample per antigen</span> |
|
| 141 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 126 × 21</span></span> |
|
| 142 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: antigen [6]</span></span> |
|
| 143 |
+<span class="r-out co"><span class="r-pr">#></span> antigen sampleID sampl…¹ meanX meanX…² meanX…³ meanX…⁴ sdX sdX2_X3 sdX1_X3</span> |
|
| 144 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span> |
|
| 145 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> AMA1 0.0085 11 643. 594. 692 642. 98.5 70 69.3</span> |
|
| 146 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> AMA1 0.0255 8 699 700. 672 724. 52.6 74.2 33.9</span> |
|
| 147 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> AMA1 0.076 5 633. 588 668. 642. 81.3 35.4 77.1</span> |
|
| 148 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> AMA1 0.23 2 <span style="text-decoration: underline;">1</span>725. <span style="text-decoration: underline;">1</span>757 <span style="text-decoration: underline;">1</span>720 <span style="text-decoration: underline;">1</span>697 60.5 32.5 84.8</span> |
|
| 149 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> AMA1 0.73 19 <span style="text-decoration: underline;">2</span>504. <span style="text-decoration: underline;">2</span>494. <span style="text-decoration: underline;">2</span>568. <span style="text-decoration: underline;">2</span>450 119. 166. 61.5</span> |
|
| 150 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> AMA1 177.78 4 <span style="text-decoration: underline;">58</span>262 <span style="text-decoration: underline;">58</span>208 <span style="text-decoration: underline;">58</span>640. <span style="text-decoration: underline;">57</span>938. 709. 994. 383. </span> |
|
| 151 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> AMA1 19.75 10 <span style="text-decoration: underline;">64</span>143. <span style="text-decoration: underline;">64</span>204. <span style="text-decoration: underline;">64</span>280. <span style="text-decoration: underline;">63</span>944 353. 476. 367. </span> |
|
| 152 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> AMA1 2.19 16 <span style="text-decoration: underline;">9</span>243 <span style="text-decoration: underline;">9</span>294 <span style="text-decoration: underline;">9</span>031 <span style="text-decoration: underline;">9</span>404 383. 528. 156. </span> |
|
| 153 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> AMA1 533 1 <span style="text-decoration: underline;">53</span>180. <span style="text-decoration: underline;">52</span>860. <span style="text-decoration: underline;">53</span>298 <span style="text-decoration: underline;">53</span>380. 559. 117. 735. </span> |
|
| 154 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> AMA1 59.26 7 <span style="text-decoration: underline;">61</span>601 <span style="text-decoration: underline;">61</span>870. <span style="text-decoration: underline;">61</span>848. <span style="text-decoration: underline;">61</span>085 894. <span style="text-decoration: underline;">1</span>078. <span style="text-decoration: underline;">1</span>111. </span> |
|
| 155 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 116 more rows, 11 more variables: sdX1_X2 <dbl>, CVX <dbl>,</span></span> |
|
| 156 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CVX2_X3 <dbl>, CVX1_X3 <dbl>, CVX1_X2 <dbl>, cvCat_all <chr>,</span></span> |
|
| 157 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># cvSelected_all <dbl>, iden <chr>, `1` <dbl>, `2` <dbl>, `3` <dbl>, and</span></span> |
|
| 158 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># abbreviated variable names ¹sample_array_ID, ²meanX2_X3, ³meanX1_X3,</span></span> |
|
| 159 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ⁴meanX1_X2</span></span> |
|
| 160 |
+</code></pre></div> |
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| 161 |
+ </div> |
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+ </div> |
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+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |
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+ <footer><div class="copyright"> |
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+ <p></p><p>Developed by Kennedy Mwai, James Mburu.</p> |
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+ |
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+<div class="pkgdown"> |
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+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> |
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+ <h1>\\_Start_Function_For Error\\ #</h1> |
|
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+ <small class="dont-index">Source: <a href="https://github.com/Keniajin/protGear/blob/HEAD/R/global_functions.R" class="external-link"><code>R/global_functions.R</code></a></small> |
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+ <div class="hidden name"><code>error_replicates.Rd</code></div> |
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+ </div> |
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+ |
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+ <div class="ref-description"> |
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+ <p>A generic function to write into the log |
|
| 64 |
+file with a replicate check error</p> |
|
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+ </div> |
|
| 66 |
+ |
|
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+ <div id="ref-usage"> |
|
| 68 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">error_replicates</span><span class="op">(</span><span class="va">iden</span><span class="op">)</span></span></code></pre></div> |
|
| 69 |
+ </div> |
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+ |
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+ <div id="arguments"> |
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+ <dl><dt>iden</dt> |
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+<dd><p>An id for the file with replicates error</p></dd> |
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+ |
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+</dl></div> |
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+ <div id="value"> |
|
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+ <h2>Value</h2> |
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+ |
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+ |
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| 81 |
+<p>a log file showing the replicate errors</p> |
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+ </div> |
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+data for micro array data."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> |
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+<li> |
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+ |
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+ </header><div class="row"> |
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+ <div class="col-md-9 contents"> |
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+ <div class="page-header"> |
|
| 57 |
+ <h1>extract bg</h1> |
|
| 58 |
+ <small class="dont-index">Source: <a href="https://github.com/Keniajin/protGear/blob/HEAD/R/read_files_functions.R" class="external-link"><code>R/read_files_functions.R</code></a></small> |
|
| 59 |
+ <div class="hidden name"><code>extract_bg.Rd</code></div> |
|
| 60 |
+ </div> |
|
| 61 |
+ |
|
| 62 |
+ <div class="ref-description"> |
|
| 63 |
+ <p>A generic function to extract the background |
|
| 64 |
+data for micro array data.</p> |
|
| 65 |
+ </div> |
|
| 66 |
+ |
|
| 67 |
+ <div id="ref-usage"> |
|
| 68 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">extract_bg</span><span class="op">(</span><span class="va">iden</span>, <span class="va">data_files</span>, genepix_vars <span class="op">=</span> <span class="va">genepix_vars</span><span class="op">)</span></span></code></pre></div> |
|
| 69 |
+ </div> |
|
| 70 |
+ |
|
| 71 |
+ <div id="arguments"> |
|
| 72 |
+ <h2>Arguments</h2> |
|
| 73 |
+ <dl><dt>iden</dt> |
|
| 74 |
+<dd><p>A character indicating the name of the object to be |
|
| 75 |
+used under data_files.</p></dd> |
|
| 76 |
+ |
|
| 77 |
+ |
|
| 78 |
+<dt>data_files</dt> |
|
| 79 |
+<dd><p>A list of data objects with names utilised by iden.</p></dd> |
|
| 80 |
+ |
|
| 81 |
+ |
|
| 82 |
+<dt>genepix_vars</dt> |
|
| 83 |
+<dd><p>A list of specific definitions of the experiment design. |
|
| 84 |
+See <code><a href="array_vars.html">array_vars</a></code>.</p></dd> |
|
| 85 |
+ |
|
| 86 |
+</dl></div> |
|
| 87 |
+ <div id="value"> |
|
| 88 |
+ <h2>Value</h2> |
|
| 89 |
+ |
|
| 90 |
+ |
|
| 91 |
+<p>A data frame of background values</p> |
|
| 92 |
+ </div> |
|
| 93 |
+ <div id="details"> |
|
| 94 |
+ <h2>Details</h2> |
|
| 95 |
+ <p>Extract the background values</p> |
|
| 96 |
+ </div> |
|
| 97 |
+ |
|
| 98 |
+ <div id="ref-examples"> |
|
| 99 |
+ <h2>Examples</h2> |
|
| 100 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co">## Not run:</span></span></span> |
|
| 101 |
+<span class="r-in"><span><span class="va">genepix_vars</span> <span class="op"><-</span> <span class="fu"><a href="array_vars.html">array_vars</a></span><span class="op">(</span></span></span> |
|
| 102 |
+<span class="r-in"><span>channel <span class="op">=</span> <span class="st">"635"</span>,</span></span> |
|
| 103 |
+<span class="r-in"><span>chip_path <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata"</span>, <span class="st">"array_data/machine1/"</span>, </span></span> |
|
| 104 |
+<span class="r-in"><span>package<span class="op">=</span><span class="st">"protGear"</span><span class="op">)</span>,</span></span> |
|
| 105 |
+<span class="r-in"><span>totsamples <span class="op">=</span> <span class="fl">21</span>,</span></span> |
|
| 106 |
+<span class="r-in"><span>blockspersample <span class="op">=</span> <span class="fl">2</span>,</span></span> |
|
| 107 |
+<span class="r-in"><span>mig_prefix <span class="op">=</span> <span class="st">"_first"</span>,</span></span> |
|
| 108 |
+<span class="r-in"><span>machine <span class="op">=</span> <span class="fl">1</span>,</span></span> |
|
| 109 |
+<span class="r-in"><span><span class="co">## optional</span></span></span> |
|
| 110 |
+<span class="r-in"><span>date_process <span class="op">=</span> <span class="st">"0520"</span></span></span> |
|
| 111 |
+<span class="r-in"><span><span class="op">)</span></span></span> |
|
| 112 |
+<span class="r-in"><span><span class="co">#Define the data path</span></span></span> |
|
| 113 |
+<span class="r-in"><span><span class="va">data_path</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">genepix_vars</span><span class="op">$</span><span class="va">chip_path</span><span class="op">)</span></span></span> |
|
| 114 |
+<span class="r-in"><span><span class="co"># List the file names to use</span></span></span> |
|
| 115 |
+<span class="r-in"><span><span class="va">filenames</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.files.html" class="external-link">list.files</a></span><span class="op">(</span><span class="va">genepix_vars</span><span class="op">$</span><span class="va">chip_path</span>,</span></span> |
|
| 116 |
+<span class="r-in"><span> pattern <span class="op">=</span> <span class="st">'*.txt$|*.gpr$'</span>, full.names <span class="op">=</span> <span class="cn">FALSE</span></span></span> |
|
| 117 |
+<span class="r-in"><span><span class="op">)</span></span></span> |
|
| 118 |
+<span class="r-in"><span><span class="va">data_files</span> <span class="op"><-</span> <span class="fu">purrr</span><span class="fu">::</span><span class="fu"><a href="https://purrr.tidyverse.org/reference/map.html" class="external-link">map</a></span><span class="op">(</span></span></span> |
|
| 119 |
+<span class="r-in"><span> .x <span class="op">=</span> <span class="va">filenames</span>,</span></span> |
|
| 120 |
+<span class="r-in"><span> .f <span class="op">=</span> <span class="va">read_array_files</span>,</span></span> |
|
| 121 |
+<span class="r-in"><span> data_path <span class="op">=</span> <span class="va">data_path</span>,</span></span> |
|
| 122 |
+<span class="r-in"><span> genepix_vars <span class="op">=</span> <span class="va">genepix_vars</span></span></span> |
|
| 123 |
+<span class="r-in"><span><span class="op">)</span></span></span> |
|
| 124 |
+<span class="r-in"><span><span class="va">data_files</span> <span class="op"><-</span> <span class="fu">purrr</span><span class="fu">::</span><span class="fu"><a href="https://rlang.r-lib.org/reference/set_names.html" class="external-link">set_names</a></span><span class="op">(</span><span class="va">data_files</span>, </span></span> |
|
| 125 |
+<span class="r-in"><span><span class="fu">purrr</span><span class="fu">::</span><span class="fu"><a href="https://purrr.tidyverse.org/reference/map.html" class="external-link">map</a></span><span class="op">(</span><span class="va">filenames</span>, <span class="va">name_of_files</span><span class="op">)</span><span class="op">)</span></span></span> |
|
| 126 |
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">data_files</span><span class="op">)</span></span></span> |
|
| 127 |
+<span class="r-out co"><span class="r-pr">#></span> [1] "BRB001" "KK2-06"</span> |
|
| 128 |
+<span class="r-in"><span><span class="fu">extract_bg</span><span class="op">(</span>iden <span class="op">=</span><span class="st">"KK2-06"</span> , data_files<span class="op">=</span><span class="va">data_files</span>,genepix_vars<span class="op">=</span><span class="va">genepix_vars</span><span class="op">)</span></span></span> |
|
| 129 |
+<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>KK2-06 Not found in the sampleID files heredata/array_sampleID/</span> |
|
| 130 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 7,245 × 6</span></span> |
|
| 131 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: sampleID, antigen [2,415]</span></span> |
|
| 132 |
+<span class="r-out co"><span class="r-pr">#></span> sampleID antigen Block FBG_Median BG_Median replicate</span> |
|
| 133 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span></span> |
|
| 134 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> SID_gen1 MSP3.6 1 <span style="text-decoration: underline;">5</span>488 <span style="text-decoration: underline;">1</span>126 1</span> |
|
| 135 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> SID_gen1 ETRAMP10.2 1 <span style="text-decoration: underline;">6</span>350 <span style="text-decoration: underline;">1</span>026 1</span> |
|
| 136 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> SID_gen1 GAMA 1 <span style="text-decoration: underline;">15</span>768 <span style="text-decoration: underline;">1</span>059 1</span> |
|
| 137 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> SID_gen1 MSRP4 1 <span style="text-decoration: underline;">65</span>535 <span style="text-decoration: underline;">1</span>413 1</span> |
|
| 138 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> SID_gen1 MSP4 1 <span style="text-decoration: underline;">65</span>535 <span style="text-decoration: underline;">1</span>405 1</span> |
|
| 139 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> SID_gen1 RAMA 1 <span style="text-decoration: underline;">43</span>966 <span style="text-decoration: underline;">1</span>085 1</span> |
|
| 140 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> SID_gen1 ASP 1 <span style="text-decoration: underline;">65</span>535 <span style="text-decoration: underline;">1</span>092 1</span> |
|
| 141 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> SID_gen1 MSP3.6 1 <span style="text-decoration: underline;">6</span>596 <span style="text-decoration: underline;">1</span>343 2</span> |
|
| 142 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> SID_gen1 ETRAMP10.2 1 <span style="text-decoration: underline;">7</span>123 <span style="text-decoration: underline;">1</span>136 2</span> |
|
| 143 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> SID_gen1 GAMA 1 <span style="text-decoration: underline;">17</span>420 <span style="text-decoration: underline;">1</span>311 2</span> |
|
| 144 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 7,235 more rows</span></span> |
|
| 145 |
+<span class="r-in"><span><span class="co">## End(Not run)</span></span></span> |
|
| 146 |
+</code></pre></div> |
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+ </div> |
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+ </div> |
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+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |
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+ <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> |
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+ </nav></div> |
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+</div> |
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+ <footer><div class="copyright"> |
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+ <p></p><p>Developed by Kennedy Mwai, James Mburu.</p> |
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+ |
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+<div class="pkgdown"> |
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+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> |
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+ </body></html> |
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new file mode 100644 |
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Function reference • protGear</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Function reference"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> |
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+ </a> |
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+ <ul class="dropdown-menu" role="menu"><li> |
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+ <a href="../articles/vignette.html">protGear vignette processing suite</a> |
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+ </li> |
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+ </ul></li> |
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+<li> |
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+ <a href="../news/index.html">Changelog</a> |
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+</li> |
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+ </ul><ul class="nav navbar-nav navbar-right"><li> |
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+ |
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+ </a> |
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+</li> |
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+ </ul></div><!--/.nav-collapse --> |
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+ </div><!--/.container --> |
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+</div><!--/.navbar --> |
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+ |
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+ |
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+ |
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+ </header><div class="row"> |
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+ <div class="contents col-md-9"> |
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+ <div class="page-header"> |
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+ <h1>Reference</h1> |
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+ </div> |
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+ |
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| 59 |
+ <table class="ref-index"><colgroup><col class="alias"><col class="title"></colgroup><tbody><tr><th colspan="2"> |
|
| 60 |
+ <h2 id="all-functions">All functions <a href="#all-functions" class="anchor" aria-hidden="true"></a></h2> |
|
| 61 |
+ <p class="section-desc"></p> |
|
| 62 |
+ </th> |
|
| 63 |
+ </tr></tbody><tbody><tr><td> |
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| 64 |
+ <p><code><a href="array_vars.html">array_vars()</a></code> </p> |
|
| 65 |
+ </td> |
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| 66 |
+ <td><p>List the array structure variables</p></td> |
|
| 67 |
+ </tr><tr><td> |
|
| 68 |
+ <p><code><a href="best_CV_estimation.html">best_CV_estimation()</a></code> </p> |
|
| 69 |
+ </td> |
|
| 70 |
+ <td><p>best CV estimation</p></td> |
|
| 71 |
+ </tr><tr><td> |
|
| 72 |
+ <p><code><a href="bg_correct.html">bg_correct()</a></code> </p> |
|
| 73 |
+ </td> |
|
| 74 |
+ <td><p>bg_correct</p></td> |
|
| 75 |
+ </tr><tr><td> |
|
| 76 |
+ <p><code><a href="buffer_spots.html">buffer_spots()</a></code> </p> |
|
| 77 |
+ </td> |
|
| 78 |
+ <td><p>Extract buffer spots of data</p></td> |
|
| 79 |
+ </tr><tr><td> |
|
| 80 |
+ <p><code><a href="check_sampleID_files.html">check_sampleID_files()</a></code> </p> |
|
| 81 |
+ </td> |
|
| 82 |
+ <td><p>\\_End_Function_\\ # |
|
| 83 |
+Check existing sample ID names</p></td> |
|
| 84 |
+ </tr><tr><td> |
|
| 85 |
+ <p><code><a href="create_dir.html">create_dir()</a></code> </p> |
|
| 86 |
+ </td> |
|
| 87 |
+ <td><p>Title Create directory function</p></td> |
|
| 88 |
+ </tr><tr><td> |
|
| 89 |
+ <p><code><a href="cv_by_sample_estimation.html">cv_by_sample_estimation()</a></code> </p> |
|
| 90 |
+ </td> |
|
| 91 |
+ <td><p>cv by sample</p></td> |
|
| 92 |
+ </tr><tr><td> |
|
| 93 |
+ <p><code><a href="cv_estimation.html">cv_estimation()</a></code> </p> |
|
| 94 |
+ </td> |
|
| 95 |
+ <td><p>cv_estimation</p></td> |
|
| 96 |
+ </tr><tr><td> |
|
| 97 |
+ <p><code><a href="extract_bg.html">extract_bg()</a></code> </p> |
|
| 98 |
+ </td> |
|
| 99 |
+ <td><p>extract bg</p></td> |
|
| 100 |
+ </tr><tr><td> |
|
| 101 |
+ <p><code><a href="launch_protGear_interactive.html">launch_protGear_interactive()</a></code> </p> |
|
| 102 |
+ </td> |
|
| 103 |
+ <td><p>launch_protGear_interactive</p></td> |
|
| 104 |
+ </tr><tr><td> |
|
| 105 |
+ <p><code><a href="launch_select.html">launch_select()</a></code> </p> |
|
| 106 |
+ </td> |
|
| 107 |
+ <td><p>launch_select</p></td> |
|
| 108 |
+ </tr><tr><td> |
|
| 109 |
+ <p><code><a href="matrix_normalise.html">matrix_normalise()</a></code> </p> |
|
| 110 |
+ </td> |
|
| 111 |
+ <td><p>Normalize Arrays</p></td> |
|
| 112 |
+ </tr><tr><td> |
|
| 113 |
+ <p><code><a href="merge_sampleID.html">merge_sampleID()</a></code> </p> |
|
| 114 |
+ </td> |
|
| 115 |
+ <td><p>Merge sample ID with the array data</p></td> |
|
| 116 |
+ </tr><tr><td> |
|
| 117 |
+ <p><code><a href="minpositive.html">minpositive()</a></code> </p> |
|
| 118 |
+ </td> |
|
| 119 |
+ <td><p>Get the minimum positive value</p></td> |
|
| 120 |
+ </tr><tr><td> |
|
| 121 |
+ <p><code><a href="name_of_files.html">name_of_files()</a></code> </p> |
|
| 122 |
+ </td> |
|
| 123 |
+ <td><p>Object names of a list</p></td> |
|
| 124 |
+ </tr><tr><td> |
|
| 125 |
+ <p><code><a href="output_trend_stats.html">output_trend_stats()</a></code> </p> |
|
| 126 |
+ </td> |
|
| 127 |
+ <td><p>Trend test using Cox–Stuart (C–S) and Mann–Kendall (M–K) trend tests</p></td> |
|
| 128 |
+ </tr><tr><td> |
|
| 129 |
+ <p><code><a href="plot_bg.html">plot_bg()</a></code> </p> |
|
| 130 |
+ </td> |
|
| 131 |
+ <td><p>Plot background</p></td> |
|
| 132 |
+ </tr><tr><td> |
|
| 133 |
+ <p><code><a href="plot_buffer.html">plot_buffer()</a></code> </p> |
|
| 134 |
+ </td> |
|
| 135 |
+ <td><p>Plot the buffer values</p></td> |
|
| 136 |
+ </tr><tr><td> |
|
| 137 |
+ <p><code><a href="plot_FB.html">plot_FB()</a></code> </p> |
|
| 138 |
+ </td> |
|
| 139 |
+ <td><p>plot_FB</p></td> |
|
| 140 |
+ </tr><tr><td> |
|
| 141 |
+ <p><code><a href="plot_normalised.html">plot_normalised()</a></code> </p> |
|
| 142 |
+ </td> |
|
| 143 |
+ <td><p>Comparison of normalised data by sample</p></td> |
|
| 144 |
+ </tr><tr><td> |
|
| 145 |
+ <p><code><a href="plot_normalised_antigen.html">plot_normalised_antigen()</a></code> </p> |
|
| 146 |
+ </td> |
|
| 147 |
+ <td><p>Comparison of normalised data by feature</p></td> |
|
| 148 |
+ </tr><tr><td> |
|
| 149 |
+ <p><code><a href="read_array_files.html">read_array_files()</a></code> </p> |
|
| 150 |
+ </td> |
|
| 151 |
+ <td><p>Read array files</p></td> |
|
| 152 |
+ </tr><tr><td> |
|
| 153 |
+ <p><code><a href="read_array_visualize.html">read_array_visualize()</a></code> </p> |
|
| 154 |
+ </td> |
|
| 155 |
+ <td><p>Read a gpr file to visualize</p></td> |
|
| 156 |
+ </tr><tr><td> |
|
| 157 |
+ <p><code><a href="rlm_normalise_matrix.html">rlm_normalise_matrix()</a></code> </p> |
|
| 158 |
+ </td> |
|
| 159 |
+ <td><p>Nomrmalise using RLM</p></td> |
|
| 160 |
+ </tr><tr><td> |
|
| 161 |
+ <p><code><a href="tag_subtract.html">tag_subtract()</a></code> </p> |
|
| 162 |
+ </td> |
|
| 163 |
+ <td><p>tag_subtract</p></td> |
|
| 164 |
+ </tr><tr><td> |
|
| 165 |
+ <p><code><a href="visualize_slide.html">visualize_slide()</a></code> </p> |
|
| 166 |
+ </td> |
|
| 167 |
+ <td><p>Visualize the slide mimicking the original scan image.</p></td> |
|
| 168 |
+ </tr><tr><td> |
|
| 169 |
+ <p><code><a href="visualize_slide_2d.html">visualize_slide_2d()</a></code> </p> |
|
| 170 |
+ </td> |
|
| 171 |
+ <td><p>Visualize the slide mimicking the original scan image using a 2d plot.</p></td> |
|
| 172 |
+ </tr></tbody></table></div> |
|
| 173 |
+ |
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+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |
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+ <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> |
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+ </nav></div> |
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+ <p></p><p>Developed by Kennedy Mwai, James Mburu.</p> |
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+ |
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+<div class="pkgdown"> |
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+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> |
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>launch_protGear_interactive — launch_protGear_interactive • protGear</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="launch_protGear_interactive — launch_protGear_interactive"><meta property="og:description" content="This is Function is to launch the shiny application"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> |
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+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> |
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+ <a class="navbar-link" href="../index.html">protGear</a> |
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+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.2.1</span> |
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+ </a> |
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+ <ul class="dropdown-menu" role="menu"><li> |
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+ <a href="../articles/vignette.html">protGear vignette processing suite</a> |
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+ </li> |
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+ </ul></li> |
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+<li> |
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+ <a href="../news/index.html">Changelog</a> |
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+</li> |
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+ </ul><ul class="nav navbar-nav navbar-right"><li> |
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+ <a href="https://github.com/Keniajin/protGear/" class="external-link"> |
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+ <span class="fab fa-github fa-lg"></span> |
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+ |
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+ <div class="col-md-9 contents"> |
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+ <div class="page-header"> |
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+ <h1>launch_protGear_interactive</h1> |
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+ <small class="dont-index">Source: <a href="https://github.com/Keniajin/protGear/blob/HEAD/R/launch_protGear_interactive.R" class="external-link"><code>R/launch_protGear_interactive.R</code></a></small> |
|
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+ <div class="hidden name"><code>launch_protGear_interactive.Rd</code></div> |
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+ </div> |
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+ |
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+ <div class="ref-description"> |
|
| 62 |
+ <p>This is Function is to launch the shiny application</p> |
|
| 63 |
+ </div> |
|
| 64 |
+ |
|
| 65 |
+ <div id="ref-usage"> |
|
| 66 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">launch_protGear_interactive</span><span class="op">(</span><span class="op">)</span></span></code></pre></div> |
|
| 67 |
+ </div> |
|
| 68 |
+ |
|
| 69 |
+ <div id="value"> |
|
| 70 |
+ <h2>Value</h2> |
|
| 71 |
+ |
|
| 72 |
+ |
|
| 73 |
+<p>launches the shiny interactive protGear app</p> |
|
| 74 |
+ </div> |
|
| 75 |
+ |
|
| 76 |
+ <div id="ref-examples"> |
|
| 77 |
+ <h2>Examples</h2> |
|
| 78 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">app</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"shiny-examples"</span>, <span class="st">"protGear_interactive"</span>,</span></span> |
|
| 79 |
+<span class="r-in"><span><span class="st">"protGear_interactive.Rmd"</span>, package <span class="op">=</span> <span class="st">"protGear"</span><span class="op">)</span></span></span> |
|
| 80 |
+<span class="r-in"><span> <span class="kw">if</span> <span class="op">(</span><span class="va">app</span><span class="op">!=</span><span class="st">""</span><span class="op">)</span><span class="op">{</span></span></span>
|
|
| 81 |
+<span class="r-in"><span> <span class="co">## run this</span></span></span> |
|
| 82 |
+<span class="r-in"><span> <span class="co">#launch_protGear_interactive()</span></span></span> |
|
| 83 |
+<span class="r-in"><span> <span class="op">}</span></span></span> |
|
| 84 |
+<span class="r-out co"><span class="r-pr">#></span> NULL</span> |
|
| 85 |
+<span class="r-in"><span></span></span> |
|
| 86 |
+</code></pre></div> |
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| 87 |
+ </div> |
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+ </div> |
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+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |
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+ <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> |
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+ <p></p><p>Developed by Kennedy Mwai, James Mburu.</p> |
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+<div class="pkgdown"> |
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+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> |
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+ </body></html> |
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new file mode 100644 |
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>launch_select — launch_select • protGear</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="launch_select — launch_select"><meta property="og:description" content="This is Function is to launch mutiple shiny applications for protGear"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> |
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+ <div class="col-md-9 contents"> |
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| 55 |
+ <div class="page-header"> |
|
| 56 |
+ <h1>launch_select</h1> |
|
| 57 |
+ <small class="dont-index">Source: <a href="https://github.com/Keniajin/protGear/blob/HEAD/R/launch_protGear_interactive.R" class="external-link"><code>R/launch_protGear_interactive.R</code></a></small> |
|
| 58 |
+ <div class="hidden name"><code>launch_select.Rd</code></div> |
|
| 59 |
+ </div> |
|
| 60 |
+ |
|
| 61 |
+ <div class="ref-description"> |
|
| 62 |
+ <p>This is Function is to launch mutiple shiny applications for protGear</p> |
|
| 63 |
+ </div> |
|
| 64 |
+ |
|
| 65 |
+ <div id="ref-usage"> |
|
| 66 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">launch_select</span><span class="op">(</span><span class="va">theApp</span><span class="op">)</span></span></code></pre></div> |
|
| 67 |
+ </div> |
|
| 68 |
+ |
|
| 69 |
+ <div id="arguments"> |
|
| 70 |
+ <h2>Arguments</h2> |
|
| 71 |
+ <dl><dt>theApp</dt> |
|
| 72 |
+<dd><p>accepts one of the folders containing the shiny appplication</p></dd> |
|
| 73 |
+ |
|
| 74 |
+</dl></div> |
|
| 75 |
+ <div id="value"> |
|
| 76 |
+ <h2>Value</h2> |
|
| 77 |
+ |
|
| 78 |
+ |
|
| 79 |
+<p>launches the app defined under theApp</p> |
|
| 80 |
+ </div> |
|
| 81 |
+ |
|
| 82 |
+ <div id="ref-examples"> |
|
| 83 |
+ <h2>Examples</h2> |
|
| 84 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">validExamples</span> <span class="op"><-</span></span></span> |
|
| 85 |
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/list.files.html" class="external-link">list.files</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"shiny-examples"</span>, package <span class="op">=</span> <span class="st">"protGear"</span><span class="op">)</span><span class="op">)</span></span></span> |
|
| 86 |
+<span class="r-in"><span><span class="co">#launch_select(validExamples[[1]])</span></span></span> |
|
| 87 |
+</code></pre></div> |
|
| 88 |
+ </div> |
|
| 89 |
+ </div> |
|
| 90 |
+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |
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| 91 |
+ <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> |
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| 92 |
+ </nav></div> |
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+</div> |
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| 94 |
+ |
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+ |
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+ <footer><div class="copyright"> |
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+ <p></p><p>Developed by Kennedy Mwai, James Mburu.</p> |
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+</div> |
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+ |
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+<div class="pkgdown"> |
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+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> |
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+ </body></html> |
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+ |
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new file mode 100644 |
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+<!DOCTYPE html> |
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Normalize Arrays — matrix_normalise • protGear</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Normalize Arrays — matrix_normalise"><meta property="og:description" content="Normalize Arrays"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> |
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+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> |
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+<![endif]--></head><body data-spy="scroll" data-target="#toc"> |
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+ <a class="navbar-link" href="../index.html">protGear</a> |
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+ <div class="col-md-9 contents"> |
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+ <div class="page-header"> |
|
| 56 |
+ <h1>Normalize Arrays</h1> |
|
| 57 |
+ <small class="dont-index">Source: <a href="https://github.com/Keniajin/protGear/blob/HEAD/R/normalisation_functions.R" class="external-link"><code>R/normalisation_functions.R</code></a></small> |
|
| 58 |
+ <div class="hidden name"><code>matrix_normalise.Rd</code></div> |
|
| 59 |
+ </div> |
|
| 60 |
+ |
|
| 61 |
+ <div class="ref-description"> |
|
| 62 |
+ <p>Normalize Arrays</p> |
|
| 63 |
+ </div> |
|
| 64 |
+ |
|
| 65 |
+ <div id="ref-usage"> |
|
| 66 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">matrix_normalise</span><span class="op">(</span></span> |
|
| 67 |
+<span> <span class="va">matrix_antigen</span>,</span> |
|
| 68 |
+<span> method <span class="op">=</span> <span class="st">"log2"</span>,</span> |
|
| 69 |
+<span> batch_correct <span class="op">=</span> <span class="cn">FALSE</span>,</span> |
|
| 70 |
+<span> <span class="va">batch_var1</span>,</span> |
|
| 71 |
+<span> batch_var2 <span class="op">=</span> <span class="va">day_batches</span>,</span> |
|
| 72 |
+<span> return_plot <span class="op">=</span> <span class="cn">FALSE</span>,</span> |
|
| 73 |
+<span> plot_by_antigen <span class="op">=</span> <span class="cn">TRUE</span>,</span> |
|
| 74 |
+<span> control_antigens <span class="op">=</span> <span class="cn">NULL</span>,</span> |
|
| 75 |
+<span> array_matrix <span class="op">=</span> <span class="cn">NULL</span></span> |
|
| 76 |
+<span><span class="op">)</span></span></code></pre></div> |
|
| 77 |
+ </div> |
|
| 78 |
+ |
|
| 79 |
+ <div id="arguments"> |
|
| 80 |
+ <h2>Arguments</h2> |
|
| 81 |
+ <dl><dt>matrix_antigen</dt> |
|
| 82 |
+<dd><p>An object of class matrix with features/proteins as |
|
| 83 |
+columns and samples as the rows</p></dd> |
|
| 84 |
+ |
|
| 85 |
+ |
|
| 86 |
+<dt>method</dt> |
|
| 87 |
+<dd><p>character string specifying the normalization method. |
|
| 88 |
+ Choices are <code>"none","log2","vsn","cyclic_loess"</code> |
|
| 89 |
+<code>"cyclic_loess_log" ,"rlm"</code></p></dd> |
|
| 90 |
+ |
|
| 91 |
+ |
|
| 92 |
+<dt>batch_correct</dt> |
|
| 93 |
+<dd><p>A logical value indicating whether batch |
|
| 94 |
+correction should be done or not</p></dd> |
|
| 95 |
+ |
|
| 96 |
+ |
|
| 97 |
+<dt>batch_var1</dt> |
|
| 98 |
+<dd><p>A character or factor vector of size similar to rows |
|
| 99 |
+of <code>matrix_antigen</code> indicating the first batch.</p></dd> |
|
| 100 |
+ |
|
| 101 |
+ |
|
| 102 |
+<dt>batch_var2</dt> |
|
| 103 |
+<dd><p>A character or factor vector of size similar to rows |
|
| 104 |
+of <code>matrix_antigen</code> indicating the second batch.</p></dd> |
|
| 105 |
+ |
|
| 106 |
+ |
|
| 107 |
+<dt>return_plot</dt> |
|
| 108 |
+<dd><p>A logical value indicating whether a plot is returned |
|
| 109 |
+to show the results of normalisation.</p></dd> |
|
| 110 |
+ |
|
| 111 |
+ |
|
| 112 |
+<dt>plot_by_antigen</dt> |
|
| 113 |
+<dd><p>Logical to indicate whether to plot by antigen or not |
|
| 114 |
+slide name for the matrix_antigen object.</p></dd> |
|
| 115 |
+ |
|
| 116 |
+ |
|
| 117 |
+<dt>control_antigens</dt> |
|
| 118 |
+<dd><p>logical vector specifying the subset of spots |
|
| 119 |
+which are non-differentially-expressed control spots, |
|
| 120 |
+for use with <code>method="rlm"</code></p></dd> |
|
| 121 |
+ |
|
| 122 |
+ |
|
| 123 |
+<dt>array_matrix</dt> |
|
| 124 |
+<dd><p>An object of class dataframe or matrix used with |
|
| 125 |
+<code>method='rlm'</code> indicating the sample index and</p></dd> |
|
| 126 |
+ |
|
| 127 |
+</dl></div> |
|
| 128 |
+ <div id="value"> |
|
| 129 |
+ <h2>Value</h2> |
|
| 130 |
+ |
|
| 131 |
+ |
|
| 132 |
+<p>A data frame of normalised values</p> |
|
| 133 |
+ </div> |
|
| 134 |
+ |
|
| 135 |
+ <div id="ref-examples"> |
|
| 136 |
+ <h2>Examples</h2> |
|
| 137 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">matrix_antigen</span> <span class="op"><-</span> <span class="fu">readr</span><span class="fu">::</span><span class="fu"><a href="https://readr.tidyverse.org/reference/read_delim.html" class="external-link">read_csv</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata"</span>, </span></span> |
|
| 138 |
+<span class="r-in"><span><span class="st">"matrix_antigen.csv"</span>, package<span class="op">=</span><span class="st">"protGear"</span><span class="op">)</span><span class="op">)</span></span></span> |
|
| 139 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="font-weight: bold;">Rows: </span><span style="color: #0000BB;">105</span> <span style="font-weight: bold;">Columns: </span><span style="color: #0000BB;">117</span></span> |
|
| 140 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Column specification</span> <span style="color: #00BBBB;">────────────────────────────────────────────────────────</span></span> |
|
| 141 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="font-weight: bold;">Delimiter:</span> ","</span> |
|
| 142 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">dbl</span> (117): AARP, AMA1, ASP, Buffer, CD4TAG, CLAG3.2, CommercialHumanIgG, EBA...</span> |
|
| 143 |
+<span class="r-msg co"><span class="r-pr">#></span> </span> |
|
| 144 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Use `spec()` to retrieve the full column specification for this data.</span> |
|
| 145 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Specify the column types or set `show_col_types = FALSE` to quiet this message.</span> |
|
| 146 |
+<span class="r-in"><span><span class="co">#VSN</span></span></span> |
|
| 147 |
+<span class="r-in"><span><span class="va">normlise_vsn</span> <span class="op"><-</span> <span class="fu">matrix_normalise</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">as.matrix</a></span><span class="op">(</span><span class="va">matrix_antigen</span><span class="op">)</span>,</span></span> |
|
| 148 |
+<span class="r-in"><span>method <span class="op">=</span> <span class="st">"vsn"</span>,</span></span> |
|
| 149 |
+<span class="r-in"><span>return_plot <span class="op">=</span> <span class="cn">TRUE</span></span></span> |
|
| 150 |
+<span class="r-in"><span><span class="op">)</span></span></span> |
|
| 151 |
+<span class="r-in"><span><span class="co">## log</span></span></span> |
|
| 152 |
+<span class="r-in"><span><span class="va">normlise_log</span> <span class="op"><-</span> <span class="fu">matrix_normalise</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">as.matrix</a></span><span class="op">(</span><span class="va">matrix_antigen</span><span class="op">)</span>,</span></span> |
|
| 153 |
+<span class="r-in"><span>method <span class="op">=</span> <span class="st">"log2"</span>,</span></span> |
|
| 154 |
+<span class="r-in"><span>return_plot <span class="op">=</span> <span class="cn">TRUE</span></span></span> |
|
| 155 |
+<span class="r-in"><span><span class="op">)</span></span></span> |
|
| 156 |
+<span class="r-in"><span><span class="co">## cyclic_loess_log</span></span></span> |
|
| 157 |
+<span class="r-in"><span><span class="va">normlise_cylic_log</span> <span class="op"><-</span> <span class="fu">matrix_normalise</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">as.matrix</a></span><span class="op">(</span><span class="va">matrix_antigen</span><span class="op">)</span>,</span></span> |
|
| 158 |
+<span class="r-in"><span>method <span class="op">=</span> <span class="st">"cyclic_loess_log"</span>,</span></span> |
|
| 159 |
+<span class="r-in"><span>return_plot <span class="op">=</span> <span class="cn">TRUE</span></span></span> |
|
| 160 |
+<span class="r-in"><span><span class="op">)</span></span></span> |
|
| 161 |
+</code></pre></div> |
|
| 162 |
+ </div> |
|
| 163 |
+ </div> |
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| 164 |
+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |
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+ <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> |
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+ <footer><div class="copyright"> |
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+ <p></p><p>Developed by Kennedy Mwai, James Mburu.</p> |
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+ |
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+<div class="pkgdown"> |
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+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> |
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+</div> |
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+ </footer></div> |
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+ </body></html> |
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new file mode 100644 |
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Merge sample ID with the array data — merge_sampleID • protGear</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Merge sample ID with the array data — merge_sampleID"><meta property="og:description" content="A generic function that merges the protein data with the |
|
| 3 |
+ sample identifiers or sample names. If the file |
|
| 4 |
+does not have sample identifiers the function generates it automatically."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> |
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+ <a href="../articles/vignette.html">protGear vignette processing suite</a> |
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+<li> |
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+ <a href="../news/index.html">Changelog</a> |
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+ <div class="col-md-9 contents"> |
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+ <div class="page-header"> |
|
| 58 |
+ <h1>Merge sample ID with the array data</h1> |
|
| 59 |
+ <small class="dont-index">Source: <a href="https://github.com/Keniajin/protGear/blob/HEAD/R/read_files_functions.R" class="external-link"><code>R/read_files_functions.R</code></a></small> |
|
| 60 |
+ <div class="hidden name"><code>merge_sampleID.Rd</code></div> |
|
| 61 |
+ </div> |
|
| 62 |
+ |
|
| 63 |
+ <div class="ref-description"> |
|
| 64 |
+ <p>A generic function that merges the protein data with the |
|
| 65 |
+ sample identifiers or sample names. If the file |
|
| 66 |
+does not have sample identifiers the function generates it automatically.</p> |
|
| 67 |
+ </div> |
|
| 68 |
+ |
|
| 69 |
+ <div id="ref-usage"> |
|
| 70 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">merge_sampleID</span><span class="op">(</span><span class="va">iden</span>, <span class="va">data_files</span>, <span class="va">genepix_vars</span>, <span class="va">method</span><span class="op">)</span></span></code></pre></div> |
|
| 71 |
+ </div> |
|
| 72 |
+ |
|
| 73 |
+ <div id="arguments"> |
|
| 74 |
+ <h2>Arguments</h2> |
|
| 75 |
+ <dl><dt>iden</dt> |
|
| 76 |
+<dd><p>A character indicating the name of the object to be used under |
|
| 77 |
+data_files.</p></dd> |
|
| 78 |
+ |
|
| 79 |
+ |
|
| 80 |
+<dt>data_files</dt> |
|
| 81 |
+<dd><p>A list of data objects with names utilised by iden.</p></dd> |
|
| 82 |
+ |
|
| 83 |
+ |
|
| 84 |
+<dt>genepix_vars</dt> |
|
| 85 |
+<dd><p>A list of specific definitions of the experiment design. |
|
| 86 |
+See <code><a href="array_vars.html">array_vars</a></code>.</p></dd> |
|
| 87 |
+ |
|
| 88 |
+ |
|
| 89 |
+<dt>method</dt> |
|
| 90 |
+<dd><p>A description of the background correction to be used. |
|
| 91 |
+See <code><a href="bg_correct.html">bg_correct</a></code>.</p></dd> |
|
| 92 |
+ |
|
| 93 |
+</dl></div> |
|
| 94 |
+ <div id="value"> |
|
| 95 |
+ <h2>Value</h2> |
|
| 96 |
+ |
|
| 97 |
+ |
|
| 98 |
+<p>a data frame merged with corresponding sample ID's. |
|
| 99 |
+The sample ID are specified in the sample ID files</p> |
|
| 100 |
+ </div> |
|
| 101 |
+ |
|
| 102 |
+ <div id="ref-examples"> |
|
| 103 |
+ <h2>Examples</h2> |
|
| 104 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co">## Not run:</span></span></span> |
|
| 105 |
+<span class="r-in"><span><span class="co">### Define the genepix_vars</span></span></span> |
|
| 106 |
+<span class="r-in"><span><span class="va">genepix_vars</span> <span class="op"><-</span> <span class="fu"><a href="array_vars.html">array_vars</a></span><span class="op">(</span></span></span> |
|
| 107 |
+<span class="r-in"><span> channel <span class="op">=</span> <span class="st">"635"</span>,</span></span> |
|
| 108 |
+<span class="r-in"><span> chip_path <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata"</span>, <span class="st">"array_data/machine1/"</span>,</span></span> |
|
| 109 |
+<span class="r-in"><span> package<span class="op">=</span><span class="st">"protGear"</span><span class="op">)</span>,</span></span> |
|
| 110 |
+<span class="r-in"><span> totsamples <span class="op">=</span> <span class="fl">21</span>,</span></span> |
|
| 111 |
+<span class="r-in"><span> blockspersample <span class="op">=</span> <span class="fl">2</span>,</span></span> |
|
| 112 |
+<span class="r-in"><span> mig_prefix <span class="op">=</span> <span class="st">"_first"</span>,</span></span> |
|
| 113 |
+<span class="r-in"><span> machine <span class="op">=</span> <span class="fl">1</span>,</span></span> |
|
| 114 |
+<span class="r-in"><span> <span class="co">## optional</span></span></span> |
|
| 115 |
+<span class="r-in"><span> date_process <span class="op">=</span> <span class="st">"0520"</span></span></span> |
|
| 116 |
+<span class="r-in"><span><span class="op">)</span></span></span> |
|
| 117 |
+<span class="r-in"><span></span></span> |
|
| 118 |
+<span class="r-in"><span><span class="co">## the path where the micro-array data is located</span></span></span> |
|
| 119 |
+<span class="r-in"><span><span class="va">data_path</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">genepix_vars</span><span class="op">$</span><span class="va">chip_path</span><span class="op">)</span></span></span> |
|
| 120 |
+<span class="r-in"><span><span class="va">filenames</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.files.html" class="external-link">list.files</a></span><span class="op">(</span><span class="va">genepix_vars</span><span class="op">$</span><span class="va">chip_path</span>,</span></span> |
|
| 121 |
+<span class="r-in"><span> pattern <span class="op">=</span> <span class="st">"*.txt$|*.gpr$"</span>, full.names <span class="op">=</span> <span class="cn">FALSE</span></span></span> |
|
| 122 |
+<span class="r-in"><span><span class="op">)</span></span></span> |
|
| 123 |
+<span class="r-in"><span><span class="co">## create a list of all the files</span></span></span> |
|
| 124 |
+<span class="r-in"><span><span class="va">data_files</span> <span class="op"><-</span> <span class="fu">purrr</span><span class="fu">::</span><span class="fu"><a href="https://purrr.tidyverse.org/reference/map.html" class="external-link">map</a></span><span class="op">(</span></span></span> |
|
| 125 |
+<span class="r-in"><span> .x <span class="op">=</span> <span class="va">filenames</span>,</span></span> |
|
| 126 |
+<span class="r-in"><span> .f <span class="op">=</span> <span class="va">read_array_files</span>,</span></span> |
|
| 127 |
+<span class="r-in"><span> data_path <span class="op">=</span> <span class="va">data_path</span>,</span></span> |
|
| 128 |
+<span class="r-in"><span> genepix_vars <span class="op">=</span> <span class="va">genepix_vars</span></span></span> |
|
| 129 |
+<span class="r-in"><span><span class="op">)</span></span></span> |
|
| 130 |
+<span class="r-in"><span><span class="va">data_files</span> <span class="op"><-</span> <span class="fu">purrr</span><span class="fu">::</span><span class="fu"><a href="https://rlang.r-lib.org/reference/set_names.html" class="external-link">set_names</a></span><span class="op">(</span><span class="va">data_files</span>, </span></span> |
|
| 131 |
+<span class="r-in"><span><span class="fu">purrr</span><span class="fu">::</span><span class="fu"><a href="https://purrr.tidyverse.org/reference/map.html" class="external-link">map</a></span><span class="op">(</span><span class="va">filenames</span>, <span class="va">name_of_files</span><span class="op">)</span><span class="op">)</span></span></span> |
|
| 132 |
+<span class="r-in"><span><span class="co">## merge the lab data with samples and perform bg correction</span></span></span> |
|
| 133 |
+<span class="r-in"><span><span class="fu">merge_sampleID</span><span class="op">(</span>iden <span class="op">=</span> <span class="st">"KK2-06"</span>, data_files <span class="op">=</span> <span class="va">data_files</span>,</span></span> |
|
| 134 |
+<span class="r-in"><span> genepix_vars <span class="op">=</span><span class="va">genepix_vars</span>,method <span class="op">=</span> <span class="st">"subtract_global"</span> <span class="op">)</span></span></span> |
|
| 135 |
+<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>KK2-06.csv Not found in the sampleID filesdata/array_sampleID/</span> |
|
| 136 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 8,064 × 11</span></span> |
|
| 137 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: sampleID, antigen [2,457]</span></span> |
|
| 138 |
+<span class="r-out co"><span class="r-pr">#></span> sampleID sample_…¹ antigen FMedian BGMed…² FMedi…³ Block Column Row repli…⁴</span> |
|
| 139 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span></span> |
|
| 140 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> SID_gen1 1 Landma… <span style="text-decoration: underline;">65</span>535 <span style="text-decoration: underline;">2</span>443 <span style="text-decoration: underline;">64</span>413 1 1 1 1</span> |
|
| 141 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> SID_gen1 1 MSP3.6 <span style="text-decoration: underline;">5</span>488 <span style="text-decoration: underline;">1</span>126 <span style="text-decoration: underline;">4</span>366 1 2 1 1</span> |
|
| 142 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> SID_gen1 1 ETRAMP… <span style="text-decoration: underline;">6</span>350 <span style="text-decoration: underline;">1</span>026 <span style="text-decoration: underline;">5</span>228 1 3 1 1</span> |
|
| 143 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> SID_gen1 1 GAMA <span style="text-decoration: underline;">15</span>768 <span style="text-decoration: underline;">1</span>059 <span style="text-decoration: underline;">14</span>646 1 4 1 1</span> |
|
| 144 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> SID_gen1 1 MSRP4 <span style="text-decoration: underline;">65</span>535 <span style="text-decoration: underline;">1</span>413 <span style="text-decoration: underline;">64</span>413 1 5 1 1</span> |
|
| 145 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> SID_gen1 1 MSP4 <span style="text-decoration: underline;">65</span>535 <span style="text-decoration: underline;">1</span>405 <span style="text-decoration: underline;">64</span>413 1 6 1 1</span> |
|
| 146 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> SID_gen1 1 RAMA <span style="text-decoration: underline;">43</span>966 <span style="text-decoration: underline;">1</span>085 <span style="text-decoration: underline;">42</span>844 1 7 1 1</span> |
|
| 147 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> SID_gen1 1 ASP <span style="text-decoration: underline;">65</span>535 <span style="text-decoration: underline;">1</span>092 <span style="text-decoration: underline;">64</span>413 1 8 1 1</span> |
|
| 148 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> SID_gen1 1 Landma… <span style="text-decoration: underline;">65</span>535 <span style="text-decoration: underline;">4</span>198 <span style="text-decoration: underline;">64</span>413 1 1 2 2</span> |
|
| 149 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> SID_gen1 1 MSP3.6 <span style="text-decoration: underline;">6</span>596 <span style="text-decoration: underline;">1</span>343 <span style="text-decoration: underline;">5</span>474 1 2 2 2</span> |
|
| 150 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 8,054 more rows, 1 more variable: iden <chr>, and abbreviated variable</span></span> |
|
| 151 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># names ¹sample_array_ID, ²BGMedian, ³FMedianBG_correct, ⁴replicate</span></span> |
|
| 152 |
+<span class="r-in"><span><span class="co">## End(Not run)</span></span></span> |
|
| 153 |
+</code></pre></div> |
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| 154 |
+ </div> |
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+ <h1>Get the minimum positive value</h1> |
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+ <small class="dont-index">Source: <a href="https://github.com/Keniajin/protGear/blob/HEAD/R/global_functions.R" class="external-link"><code>R/global_functions.R</code></a></small> |
|
| 58 |
+ <div class="hidden name"><code>minpositive.Rd</code></div> |
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+ </div> |
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+ |
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+ <div class="ref-description"> |
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+ <p>Get the minimum positive value</p> |
|
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+ </div> |
|
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+ |
|
| 65 |
+ <div id="ref-usage"> |
|
| 66 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">minpositive</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></code></pre></div> |
|
| 67 |
+ </div> |
|
| 68 |
+ |
|
| 69 |
+ <div id="arguments"> |
|
| 70 |
+ <h2>Arguments</h2> |
|
| 71 |
+ <dl><dt>x</dt> |
|
| 72 |
+<dd><p>A numeric vector or variable</p></dd> |
|
| 73 |
+ |
|
| 74 |
+</dl></div> |
|
| 75 |
+ <div id="value"> |
|
| 76 |
+ <h2>Value</h2> |
|
| 77 |
+ |
|
| 78 |
+ |
|
| 79 |
+<p>Returns the minimum positive value in an object</p> |
|
| 80 |
+ </div> |
|
| 81 |
+ |
|
| 82 |
+ <div id="ref-examples"> |
|
| 83 |
+ <h2>Examples</h2> |
|
| 84 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">minpositive</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="op">-</span><span class="fl">1</span>,<span class="op">-</span><span class="fl">2</span>,<span class="fl">3</span>,<span class="fl">5</span>,<span class="fl">6</span>,<span class="fl">7</span>,<span class="fl">8</span>,<span class="fl">9</span>,<span class="fl">10</span><span class="op">)</span><span class="op">)</span></span></span> |
|
| 85 |
+<span class="r-out co"><span class="r-pr">#></span> [1] 3</span> |
|
| 86 |
+</code></pre></div> |
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+ </div> |
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+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |
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+ <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> |
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+ </nav></div> |
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+</div> |
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+ |
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+ <footer><div class="copyright"> |
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+ <p></p><p>Developed by Kennedy Mwai, James Mburu.</p> |
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+ |
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+<div class="pkgdown"> |
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+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> |
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Object names of a list — name_of_files • protGear</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Object names of a list — name_of_files"><meta property="og:description" content="A generic function returning a vector with the names of |
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+ <div id="navbar" class="navbar-collapse collapse"> |
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+ <ul class="nav navbar-nav"><li> |
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+ <a href="../reference/index.html">Reference</a> |
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+</li> |
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+<li class="dropdown"> |
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+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> |
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+ Articles |
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+ |
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+ <span class="caret"></span> |
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+ </a> |
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+ <ul class="dropdown-menu" role="menu"><li> |
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+ <a href="../articles/vignette.html">protGear vignette processing suite</a> |
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+ </li> |
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+ </ul></li> |
|
| 39 |
+<li> |
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+ <a href="../news/index.html">Changelog</a> |
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+</li> |
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| 42 |
+ </ul><ul class="nav navbar-nav navbar-right"><li> |
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+ <a href="https://github.com/Keniajin/protGear/" class="external-link"> |
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+ <span class="fab fa-github fa-lg"></span> |
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+ |
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+ </a> |
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| 47 |
+</li> |
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| 48 |
+ </ul></div><!--/.nav-collapse --> |
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| 49 |
+ </div><!--/.container --> |
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| 50 |
+</div><!--/.navbar --> |
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+ |
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| 52 |
+ |
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| 53 |
+ |
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| 54 |
+ </header><div class="row"> |
|
| 55 |
+ <div class="col-md-9 contents"> |
|
| 56 |
+ <div class="page-header"> |
|
| 57 |
+ <h1>Object names of a list</h1> |
|
| 58 |
+ <small class="dont-index">Source: <a href="https://github.com/Keniajin/protGear/blob/HEAD/R/global_functions.R" class="external-link"><code>R/global_functions.R</code></a></small> |
|
| 59 |
+ <div class="hidden name"><code>name_of_files.Rd</code></div> |
|
| 60 |
+ </div> |
|
| 61 |
+ |
|
| 62 |
+ <div class="ref-description"> |
|
| 63 |
+ <p>A generic function returning a vector with the names of |
|
| 64 |
+files in the same directory. Removes the file extension</p> |
|
| 65 |
+ </div> |
|
| 66 |
+ |
|
| 67 |
+ <div id="ref-usage"> |
|
| 68 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">name_of_files</span><span class="op">(</span><span class="va">i</span><span class="op">)</span></span></code></pre></div> |
|
| 69 |
+ </div> |
|
| 70 |
+ |
|
| 71 |
+ <div id="arguments"> |
|
| 72 |
+ <h2>Arguments</h2> |
|
| 73 |
+ <dl><dt>i</dt> |
|
| 74 |
+<dd><p>- a list filenames with .txt or .gpr extension</p></dd> |
|
| 75 |
+ |
|
| 76 |
+</dl></div> |
|
| 77 |
+ <div id="value"> |
|
| 78 |
+ <h2>Value</h2> |
|
| 79 |
+ |
|
| 80 |
+ |
|
| 81 |
+<p>a list of file names</p> |
|
| 82 |
+ |
|
| 83 |
+ |
|
| 84 |
+<p>name</p> |
|
| 85 |
+ </div> |
|
| 86 |
+ |
|
| 87 |
+ <div id="ref-examples"> |
|
| 88 |
+ <h2>Examples</h2> |
|
| 89 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">name_of_files</span><span class="op">(</span><span class="st">"KK2-06.txt"</span><span class="op">)</span></span></span> |
|
| 90 |
+<span class="r-out co"><span class="r-pr">#></span> [1] "KK2-06"</span> |
|
| 91 |
+</code></pre></div> |
|
| 92 |
+ </div> |
|
| 93 |
+ </div> |
|
| 94 |
+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |
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+ <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> |
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+ </nav></div> |
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+</div> |
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+ |
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| 99 |
+ |
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+ <footer><div class="copyright"> |
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| 101 |
+ <p></p><p>Developed by Kennedy Mwai, James Mburu.</p> |
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+</div> |
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| 103 |
+ |
|
| 104 |
+<div class="pkgdown"> |
|
| 105 |
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> |
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+</div> |
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+ </footer></div> |
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+ |
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+ |
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| 115 |
+ </body></html> |
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+ |
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new file mode 100644 |
| ... | ... |
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+<!DOCTYPE html> |
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Trend test using Cox–Stuart (C–S) and Mann–Kendall (M–K) trend tests — output_trend_stats • protGear</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Trend test using Cox–Stuart (C–S) and Mann–Kendall (M–K) trend tests — output_trend_stats"><meta property="og:description" content="Trend test using Cox–Stuart (C–S) and Mann–Kendall (M–K) trend tests"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> |
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+ </button> |
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+ <span class="navbar-brand"> |
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+ <a class="navbar-link" href="../index.html">protGear</a> |
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+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.2.1</span> |
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+ |
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+ <div id="navbar" class="navbar-collapse collapse"> |
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+ <ul class="nav navbar-nav"><li> |
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+</li> |
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+<li class="dropdown"> |
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+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> |
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+ Articles |
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+ |
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+ <span class="caret"></span> |
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+ </a> |
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+ <ul class="dropdown-menu" role="menu"><li> |
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+ <a href="../articles/vignette.html">protGear vignette processing suite</a> |
|
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+ </li> |
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+ </ul></li> |
|
| 38 |
+<li> |
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+ <a href="../news/index.html">Changelog</a> |
|
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+</li> |
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+ </ul><ul class="nav navbar-nav navbar-right"><li> |
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+ <a href="https://github.com/Keniajin/protGear/" class="external-link"> |
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+ <span class="fab fa-github fa-lg"></span> |
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+ |
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+ </a> |
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+</li> |
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+ </div><!--/.container --> |
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+</div><!--/.navbar --> |
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+ |
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+ |
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+ |
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+ </header><div class="row"> |
|
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+ <div class="col-md-9 contents"> |
|
| 55 |
+ <div class="page-header"> |
|
| 56 |
+ <h1>Trend test using Cox–Stuart (C–S) and Mann–Kendall (M–K) trend tests</h1> |
|
| 57 |
+ <small class="dont-index">Source: <a href="https://github.com/Keniajin/protGear/blob/HEAD/R/normalisation_functions.R" class="external-link"><code>R/normalisation_functions.R</code></a></small> |
|
| 58 |
+ <div class="hidden name"><code>output_trend_stats.Rd</code></div> |
|
| 59 |
+ </div> |
|
| 60 |
+ |
|
| 61 |
+ <div class="ref-description"> |
|
| 62 |
+ <p>Trend test using Cox–Stuart (C–S) and Mann–Kendall (M–K) trend tests</p> |
|
| 63 |
+ </div> |
|
| 64 |
+ |
|
| 65 |
+ <div id="ref-usage"> |
|
| 66 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">output_trend_stats</span><span class="op">(</span><span class="va">name</span>, <span class="va">p_val</span>, <span class="va">z_val</span><span class="op">)</span></span></code></pre></div> |
|
| 67 |
+ </div> |
|
| 68 |
+ |
|
| 69 |
+ <div id="arguments"> |
|
| 70 |
+ <h2>Arguments</h2> |
|
| 71 |
+ <dl><dt>name</dt> |
|
| 72 |
+<dd><p>Name of the test</p></dd> |
|
| 73 |
+ |
|
| 74 |
+ |
|
| 75 |
+<dt>p_val</dt> |
|
| 76 |
+<dd><p>p value from the test</p></dd> |
|
| 77 |
+ |
|
| 78 |
+ |
|
| 79 |
+<dt>z_val</dt> |
|
| 80 |
+<dd><p>the Z value of the test</p></dd> |
|
| 81 |
+ |
|
| 82 |
+</dl></div> |
|
| 83 |
+ <div id="value"> |
|
| 84 |
+ <h2>Value</h2> |
|
| 85 |
+ |
|
| 86 |
+ |
|
| 87 |
+<p>A statistics of mean standard deviation trend</p> |
|
| 88 |
+ </div> |
|
| 89 |
+ |
|
| 90 |
+ <div id="ref-examples"> |
|
| 91 |
+ <h2>Examples</h2> |
|
| 92 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">output_trend_stats</span><span class="op">(</span>name<span class="op">=</span><span class="st">"t.test"</span>,p_val<span class="op">=</span><span class="fl">0.001</span>, z_val<span class="op">=</span><span class="fl">5</span><span class="op">)</span></span></span> |
|
| 93 |
+</code></pre></div> |
|
| 94 |
+ </div> |
|
| 95 |
+ </div> |
|
| 96 |
+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |
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+ <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> |
|
| 98 |
+ </nav></div> |
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+</div> |
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| 100 |
+ |
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+ |
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+ <footer><div class="copyright"> |
|
| 103 |
+ <p></p><p>Developed by Kennedy Mwai, James Mburu.</p> |
|
| 104 |
+</div> |
|
| 105 |
+ |
|
| 106 |
+<div class="pkgdown"> |
|
| 107 |
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> |
|
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+</div> |
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+ |
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+ </footer></div> |
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+ |
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+ |
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+ |
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+ |
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+ |
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| 116 |
+ |
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| 117 |
+ </body></html> |
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+ |
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new file mode 100644 |
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+<!DOCTYPE html> |
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>plot_FB — plot_FB • protGear</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="plot_FB — plot_FB"><meta property="og:description" content="A generic function for plotting the background and foreground |
|
| 3 |
+ values."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> |
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+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> |
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+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> |
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+<![endif]--></head><body data-spy="scroll" data-target="#toc"> |
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+ |
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+ |
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+ <div class="container template-reference-topic"> |
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+ <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> |
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+ <div class="container"> |
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+ <div class="navbar-header"> |
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+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> |
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+ <span class="sr-only">Toggle navigation</span> |
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+ <span class="icon-bar"></span> |
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+ <span class="icon-bar"></span> |
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+ <a class="navbar-link" href="../index.html">protGear</a> |
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+ <div id="navbar" class="navbar-collapse collapse"> |
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+ <a href="../articles/vignette.html">protGear vignette processing suite</a> |
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+<li> |
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+ <a href="../news/index.html">Changelog</a> |
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+ <h1>plot_FB</h1> |
|
| 58 |
+ <small class="dont-index">Source: <a href="https://github.com/Keniajin/protGear/blob/HEAD/R/read_files_functions.R" class="external-link"><code>R/read_files_functions.R</code></a></small> |
|
| 59 |
+ <div class="hidden name"><code>plot_FB.Rd</code></div> |
|
| 60 |
+ </div> |
|
| 61 |
+ |
|
| 62 |
+ <div class="ref-description"> |
|
| 63 |
+ <p>A generic function for plotting the background and foreground |
|
| 64 |
+ values.</p> |
|
| 65 |
+ </div> |
|
| 66 |
+ |
|
| 67 |
+ <div id="ref-usage"> |
|
| 68 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">plot_FB</span><span class="op">(</span></span> |
|
| 69 |
+<span> <span class="va">df</span>,</span> |
|
| 70 |
+<span> antigen_name <span class="op">=</span> <span class="st">"antigen"</span>,</span> |
|
| 71 |
+<span> bg_MFI <span class="op">=</span> <span class="st">"BG_Median"</span>,</span> |
|
| 72 |
+<span> FG_MFI <span class="op">=</span> <span class="st">"FBG_Median"</span>,</span> |
|
| 73 |
+<span> log_mfi <span class="op">=</span> <span class="cn">FALSE</span></span> |
|
| 74 |
+<span><span class="op">)</span></span></code></pre></div> |
|
| 75 |
+ </div> |
|
| 76 |
+ |
|
| 77 |
+ <div id="arguments"> |
|
| 78 |
+ <h2>Arguments</h2> |
|
| 79 |
+ <dl><dt>df</dt> |
|
| 80 |
+<dd><p>An object containing the data to which the plot is done.</p></dd> |
|
| 81 |
+ |
|
| 82 |
+ |
|
| 83 |
+<dt>antigen_name</dt> |
|
| 84 |
+<dd><p>The <code>variable</code> describing which features/proteins/ |
|
| 85 |
+antibodies in the data should be used to plot</p></dd> |
|
| 86 |
+ |
|
| 87 |
+ |
|
| 88 |
+<dt>bg_MFI</dt> |
|
| 89 |
+<dd><p>A numeric <code>variable</code> describing which is the |
|
| 90 |
+background MFI</p></dd> |
|
| 91 |
+ |
|
| 92 |
+ |
|
| 93 |
+<dt>FG_MFI</dt> |
|
| 94 |
+<dd><p>A numeric <code>variable</code> describing which is the |
|
| 95 |
+foreground MFI</p></dd> |
|
| 96 |
+ |
|
| 97 |
+ |
|
| 98 |
+<dt>log_mfi</dt> |
|
| 99 |
+<dd><p>a logical value indicating whether the MFI values should be |
|
| 100 |
+log transformed or not.</p></dd> |
|
| 101 |
+ |
|
| 102 |
+</dl></div> |
|
| 103 |
+ <div id="value"> |
|
| 104 |
+ <h2>Value</h2> |
|
| 105 |
+ |
|
| 106 |
+ |
|
| 107 |
+<p>a ggplot of foreground vs background MFI values</p> |
|
| 108 |
+ </div> |
|
| 109 |
+ <div id="details"> |
|
| 110 |
+ <h2>Details</h2> |
|
| 111 |
+ <p>Plot foreground and background values</p> |
|
| 112 |
+ </div> |
|
| 113 |
+ |
|
| 114 |
+ <div id="ref-examples"> |
|
| 115 |
+ <h2>Examples</h2> |
|
| 116 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co">## Not run:</span></span></span> |
|
| 117 |
+<span class="r-in"><span><span class="co">#After extracting the background using \code{\link{extract_bg}} </span></span></span>
|
|
| 118 |
+<span class="r-in"><span><span class="co">#we plot the data using</span></span></span> |
|
| 119 |
+<span class="r-in"><span><span class="va">allData_bg</span> <span class="op"><-</span> <span class="fu">readr</span><span class="fu">::</span><span class="fu"><a href="https://readr.tidyverse.org/reference/read_delim.html" class="external-link">read_csv</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata"</span>, </span></span> |
|
| 120 |
+<span class="r-in"><span><span class="st">"bg_example.csv"</span>, package<span class="op">=</span><span class="st">"protGear"</span><span class="op">)</span><span class="op">)</span></span></span> |
|
| 121 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="font-weight: bold;">Rows: </span><span style="color: #0000BB;">126</span> <span style="font-weight: bold;">Columns: </span><span style="color: #0000BB;">6</span></span> |
|
| 122 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Column specification</span> <span style="color: #00BBBB;">────────────────────────────────────────────────────────</span></span> |
|
| 123 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="font-weight: bold;">Delimiter:</span> ","</span> |
|
| 124 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BB0000;">chr</span> (2): sampleID, antigen</span> |
|
| 125 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">dbl</span> (4): Block, FBG_Median, BG_Median, replicate</span> |
|
| 126 |
+<span class="r-msg co"><span class="r-pr">#></span> </span> |
|
| 127 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Use `spec()` to retrieve the full column specification for this data.</span> |
|
| 128 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Specify the column types or set `show_col_types = FALSE` to quiet this message.</span> |
|
| 129 |
+<span class="r-in"><span><span class="fu">plot_FB</span><span class="op">(</span><span class="va">allData_bg</span>,</span></span> |
|
| 130 |
+<span class="r-in"><span>antigen_name <span class="op">=</span> <span class="st">"antigen"</span>,</span></span> |
|
| 131 |
+<span class="r-in"><span>bg_MFI <span class="op">=</span> <span class="st">"BG_Median"</span>, FG_MFI <span class="op">=</span> <span class="st">"FBG_Median"</span>, log <span class="op">=</span> <span class="cn">FALSE</span></span></span> |
|
| 132 |
+<span class="r-in"><span><span class="op">)</span></span></span> |
|
| 133 |
+<span class="r-plt img"><img src="plot_FB-1.png" alt="" width="700" height="433"></span> |
|
| 134 |
+<span class="r-in"><span><span class="co">## End(Not run)</span></span></span> |
|
| 135 |
+</code></pre></div> |
|
| 136 |
+ </div> |
|
| 137 |
+ </div> |
|
| 138 |
+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |
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| 139 |
+ <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> |
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+ </nav></div> |
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+ <footer><div class="copyright"> |
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+ <p></p><p>Developed by Kennedy Mwai, James Mburu.</p> |
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+ |
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+<div class="pkgdown"> |
|
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+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> |
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Plot background — plot_bg • protGear</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Plot background — plot_bg"><meta property="og:description" content="A generic function for plotting of R objects."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> |
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+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> |
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+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> |
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+ <span class="icon-bar"></span> |
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+ <span class="icon-bar"></span> |
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+ </button> |
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+ <span class="navbar-brand"> |
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+ <a class="navbar-link" href="../index.html">protGear</a> |
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+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.2.1</span> |
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+ <div id="navbar" class="navbar-collapse collapse"> |
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+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> |
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+ Articles |
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+ </a> |
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+ <ul class="dropdown-menu" role="menu"><li> |
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+ <a href="../articles/vignette.html">protGear vignette processing suite</a> |
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+ </li> |
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+ </ul></li> |
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+<li> |
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+ <a href="../news/index.html">Changelog</a> |
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+</li> |
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+ </ul><ul class="nav navbar-nav navbar-right"><li> |
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+ <span class="fab fa-github fa-lg"></span> |
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+ |
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+ </a> |
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+</li> |
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+</div><!--/.navbar --> |
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+ |
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+ |
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+ |
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+ </header><div class="row"> |
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+ <div class="col-md-9 contents"> |
|
| 55 |
+ <div class="page-header"> |
|
| 56 |
+ <h1>Plot background</h1> |
|
| 57 |
+ <small class="dont-index">Source: <a href="https://github.com/Keniajin/protGear/blob/HEAD/R/read_files_functions.R" class="external-link"><code>R/read_files_functions.R</code></a></small> |
|
| 58 |
+ <div class="hidden name"><code>plot_bg.Rd</code></div> |
|
| 59 |
+ </div> |
|
| 60 |
+ |
|
| 61 |
+ <div class="ref-description"> |
|
| 62 |
+ <p>A generic function for plotting of R objects.</p> |
|
| 63 |
+ </div> |
|
| 64 |
+ |
|
| 65 |
+ <div id="ref-usage"> |
|
| 66 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">plot_bg</span><span class="op">(</span><span class="va">df</span>, x_axis <span class="op">=</span> <span class="st">"antigen"</span>, bg_MFI <span class="op">=</span> <span class="st">"BG_Median"</span>, log_mfi <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> |
|
| 67 |
+ </div> |
|
| 68 |
+ |
|
| 69 |
+ <div id="arguments"> |
|
| 70 |
+ <h2>Arguments</h2> |
|
| 71 |
+ <dl><dt>df</dt> |
|
| 72 |
+<dd><p>A default dataset to use for plot.</p></dd> |
|
| 73 |
+ |
|
| 74 |
+ |
|
| 75 |
+<dt>x_axis</dt> |
|
| 76 |
+<dd><p>The variable on the x axis</p></dd> |
|
| 77 |
+ |
|
| 78 |
+ |
|
| 79 |
+<dt>bg_MFI</dt> |
|
| 80 |
+<dd><p>A numeric <code>variable</code> describing which is the |
|
| 81 |
+background MFI</p></dd> |
|
| 82 |
+ |
|
| 83 |
+ |
|
| 84 |
+<dt>log_mfi</dt> |
|
| 85 |
+<dd><p>a logical value indicating whether the MFI values should be |
|
| 86 |
+log transformed or not.</p></dd> |
|
| 87 |
+ |
|
| 88 |
+</dl></div> |
|
| 89 |
+ <div id="value"> |
|
| 90 |
+ <h2>Value</h2> |
|
| 91 |
+ |
|
| 92 |
+ |
|
| 93 |
+<p>A ggplot of background values</p> |
|
| 94 |
+ </div> |
|
| 95 |
+ |
|
| 96 |
+ <div id="ref-examples"> |
|
| 97 |
+ <h2>Examples</h2> |
|
| 98 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co">## Not run:</span></span></span> |
|
| 99 |
+<span class="r-in"><span><span class="co">#After extracting the background using \code{\link{extract_bg}} </span></span></span>
|
|
| 100 |
+<span class="r-in"><span><span class="co">#we plot the data using</span></span></span> |
|
| 101 |
+<span class="r-in"><span><span class="va">allData_bg</span> <span class="op"><-</span> <span class="fu">readr</span><span class="fu">::</span><span class="fu"><a href="https://readr.tidyverse.org/reference/read_delim.html" class="external-link">read_csv</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata"</span>, <span class="st">"bg_example.csv"</span>,</span></span> |
|
| 102 |
+<span class="r-in"><span> package<span class="op">=</span><span class="st">"protGear"</span><span class="op">)</span><span class="op">)</span></span></span> |
|
| 103 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="font-weight: bold;">Rows: </span><span style="color: #0000BB;">126</span> <span style="font-weight: bold;">Columns: </span><span style="color: #0000BB;">6</span></span> |
|
| 104 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Column specification</span> <span style="color: #00BBBB;">────────────────────────────────────────────────────────</span></span> |
|
| 105 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="font-weight: bold;">Delimiter:</span> ","</span> |
|
| 106 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BB0000;">chr</span> (2): sampleID, antigen</span> |
|
| 107 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">dbl</span> (4): Block, FBG_Median, BG_Median, replicate</span> |
|
| 108 |
+<span class="r-msg co"><span class="r-pr">#></span> </span> |
|
| 109 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Use `spec()` to retrieve the full column specification for this data.</span> |
|
| 110 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Specify the column types or set `show_col_types = FALSE` to quiet this message.</span> |
|
| 111 |
+<span class="r-in"><span><span class="fu">plot_bg</span><span class="op">(</span><span class="va">allData_bg</span>,</span></span> |
|
| 112 |
+<span class="r-in"><span>x_axis <span class="op">=</span> <span class="st">"antigen"</span>,</span></span> |
|
| 113 |
+<span class="r-in"><span>bg_MFI <span class="op">=</span> <span class="st">"BG_Median"</span>, log_mfi <span class="op">=</span> <span class="cn">TRUE</span></span></span> |
|
| 114 |
+<span class="r-in"><span><span class="op">)</span></span></span> |
|
| 115 |
+<span class="r-plt img"><img src="plot_bg-1.png" alt="" width="700" height="433"></span> |
|
| 116 |
+<span class="r-in"><span><span class="co">## End(Not run)</span></span></span> |
|
| 117 |
+</code></pre></div> |
|
| 118 |
+ </div> |
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| 119 |
+ </div> |
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| 120 |
+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |
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+ <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> |
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+ <p></p><p>Developed by Kennedy Mwai, James Mburu.</p> |
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+ |
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+<div class="pkgdown"> |
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+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> |
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+ |
| 2 | 145 |
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+ <div class="col-md-9 contents"> |
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+ <div class="page-header"> |
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| 56 |
+ <h1>Plot the buffer values</h1> |
|
| 57 |
+ <small class="dont-index">Source: <a href="https://github.com/Keniajin/protGear/blob/HEAD/R/buffer_spot_functions.R" class="external-link"><code>R/buffer_spot_functions.R</code></a></small> |
|
| 58 |
+ <div class="hidden name"><code>plot_buffer.Rd</code></div> |
|
| 59 |
+ </div> |
|
| 60 |
+ |
|
| 61 |
+ <div class="ref-description"> |
|
| 62 |
+ <p>Plot the buffer values</p> |
|
| 63 |
+ </div> |
|
| 64 |
+ |
|
| 65 |
+ <div id="ref-usage"> |
|
| 66 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">plot_buffer</span><span class="op">(</span></span> |
|
| 67 |
+<span> df <span class="op">=</span> <span class="va">buffers</span>,</span> |
|
| 68 |
+<span> buffer_names <span class="op">=</span> <span class="st">"antigen"</span>,</span> |
|
| 69 |
+<span> buffer_mfi <span class="op">=</span> <span class="st">"FMedianBG_correct"</span>,</span> |
|
| 70 |
+<span> slide_id <span class="op">=</span> <span class="st">".id"</span></span> |
|
| 71 |
+<span><span class="op">)</span></span></code></pre></div> |
|
| 72 |
+ </div> |
|
| 73 |
+ |
|
| 74 |
+ <div id="arguments"> |
|
| 75 |
+ <h2>Arguments</h2> |
|
| 76 |
+ <dl><dt>df</dt> |
|
| 77 |
+<dd><p>A data frame to be used to plot</p></dd> |
|
| 78 |
+ |
|
| 79 |
+ |
|
| 80 |
+<dt>buffer_names</dt> |
|
| 81 |
+<dd><p>A character string containing the name of the variable |
|
| 82 |
+with buffer spots. Default set to 'antigen'.</p></dd> |
|
| 83 |
+ |
|
| 84 |
+ |
|
| 85 |
+<dt>buffer_mfi</dt> |
|
| 86 |
+<dd><p>A character string containing the name of the variable with |
|
| 87 |
+MFI value.Assuming background correction is done already. |
|
| 88 |
+Default to 'FMedianBG_correct'</p></dd> |
|
| 89 |
+ |
|
| 90 |
+ |
|
| 91 |
+<dt>slide_id</dt> |
|
| 92 |
+<dd><p>A character string containing the name of the slide/array |
|
| 93 |
+identifier variable.</p></dd> |
|
| 94 |
+ |
|
| 95 |
+</dl></div> |
|
| 96 |
+ <div id="value"> |
|
| 97 |
+ <h2>Value</h2> |
|
| 98 |
+ |
|
| 99 |
+ |
|
| 100 |
+<p>plot of buffer spots</p> |
|
| 101 |
+ </div> |
|
| 102 |
+ |
|
| 103 |
+ <div id="ref-examples"> |
|
| 104 |
+ <h2>Examples</h2> |
|
| 105 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">buffers</span> <span class="op"><-</span> <span class="fu">readr</span><span class="fu">::</span><span class="fu"><a href="https://readr.tidyverse.org/reference/read_delim.html" class="external-link">read_csv</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata"</span>, <span class="st">"buffers_sample2.csv"</span>,</span></span> |
|
| 106 |
+<span class="r-in"><span>package<span class="op">=</span><span class="st">"protGear"</span><span class="op">)</span><span class="op">)</span></span></span> |
|
| 107 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="font-weight: bold;">Rows: </span><span style="color: #0000BB;">567</span> <span style="font-weight: bold;">Columns: </span><span style="color: #0000BB;">7</span></span> |
|
| 108 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Column specification</span> <span style="color: #00BBBB;">────────────────────────────────────────────────────────</span></span> |
|
| 109 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="font-weight: bold;">Delimiter:</span> ","</span> |
|
| 110 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BB0000;">chr</span> (3): sampleID, antigen, .id</span> |
|
| 111 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">dbl</span> (4): FMedianBG_correct, Block, Column, Row</span> |
|
| 112 |
+<span class="r-msg co"><span class="r-pr">#></span> </span> |
|
| 113 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Use `spec()` to retrieve the full column specification for this data.</span> |
|
| 114 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Specify the column types or set `show_col_types = FALSE` to quiet this message.</span> |
|
| 115 |
+<span class="r-in"><span><span class="fu">plot_buffer</span><span class="op">(</span>df<span class="op">=</span><span class="va">buffers</span>,buffer_names <span class="op">=</span> <span class="st">"sampleID"</span><span class="op">)</span></span></span> |
|
| 116 |
+<span class="r-plt img"><img src="plot_buffer-1.png" alt="" width="700" height="433"></span> |
|
| 117 |
+</code></pre></div> |
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+ </div> |
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+ <p></p><p>Developed by Kennedy Mwai, James Mburu.</p> |
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Comparison of normalised data by sample — plot_normalised • protGear</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Comparison of normalised data by sample — plot_normalised"><meta property="og:description" content="Comparison of normalised data by sample"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> |
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+ <a href="../articles/vignette.html">protGear vignette processing suite</a> |
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+ </ul></li> |
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+<li> |
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+ <a href="../news/index.html">Changelog</a> |
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+</li> |
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+ </ul><ul class="nav navbar-nav navbar-right"><li> |
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+ <span class="fab fa-github fa-lg"></span> |
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+ |
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+ </a> |
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+ </ul></div><!--/.nav-collapse --> |
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+ </div><!--/.container --> |
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+</div><!--/.navbar --> |
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+ |
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+ |
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+ |
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+ </header><div class="row"> |
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+ <div class="col-md-9 contents"> |
|
| 55 |
+ <div class="page-header"> |
|
| 56 |
+ <h1>Comparison of normalised data by sample</h1> |
|
| 57 |
+ <small class="dont-index">Source: <a href="https://github.com/Keniajin/protGear/blob/HEAD/R/normalisation_functions.R" class="external-link"><code>R/normalisation_functions.R</code></a></small> |
|
| 58 |
+ <div class="hidden name"><code>plot_normalised.Rd</code></div> |
|
| 59 |
+ </div> |
|
| 60 |
+ |
|
| 61 |
+ <div class="ref-description"> |
|
| 62 |
+ <p>Comparison of normalised data by sample</p> |
|
| 63 |
+ </div> |
|
| 64 |
+ |
|
| 65 |
+ <div id="ref-usage"> |
|
| 66 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">plot_normalised</span><span class="op">(</span><span class="va">exprs_normalised_df</span>, <span class="va">method</span>, <span class="va">batch_correct</span><span class="op">)</span></span></code></pre></div> |
|
| 67 |
+ </div> |
|
| 68 |
+ |
|
| 69 |
+ <div id="arguments"> |
|
| 70 |
+ <h2>Arguments</h2> |
|
| 71 |
+ <dl><dt>exprs_normalised_df</dt> |
|
| 72 |
+<dd><p>a normalised data frame</p></dd> |
|
| 73 |
+ |
|
| 74 |
+ |
|
| 75 |
+<dt>method</dt> |
|
| 76 |
+<dd><p>the method of normalisation used</p></dd> |
|
| 77 |
+ |
|
| 78 |
+ |
|
| 79 |
+<dt>batch_correct</dt> |
|
| 80 |
+<dd><p>the batch correction</p></dd> |
|
| 81 |
+ |
|
| 82 |
+</dl></div> |
|
| 83 |
+ <div id="value"> |
|
| 84 |
+ <h2>Value</h2> |
|
| 85 |
+ |
|
| 86 |
+ |
|
| 87 |
+<p>A ggplot of normalised data</p> |
|
| 88 |
+ </div> |
|
| 89 |
+ |
|
| 90 |
+ <div id="ref-examples"> |
|
| 91 |
+ <h2>Examples</h2> |
|
| 92 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">matrix_antigen</span> <span class="op"><-</span> <span class="fu">readr</span><span class="fu">::</span><span class="fu"><a href="https://readr.tidyverse.org/reference/read_delim.html" class="external-link">read_csv</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata"</span>, </span></span> |
|
| 93 |
+<span class="r-in"><span><span class="st">"matrix_antigen.csv"</span>, package<span class="op">=</span><span class="st">"protGear"</span><span class="op">)</span><span class="op">)</span></span></span> |
|
| 94 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="font-weight: bold;">Rows: </span><span style="color: #0000BB;">105</span> <span style="font-weight: bold;">Columns: </span><span style="color: #0000BB;">117</span></span> |
|
| 95 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Column specification</span> <span style="color: #00BBBB;">────────────────────────────────────────────────────────</span></span> |
|
| 96 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="font-weight: bold;">Delimiter:</span> ","</span> |
|
| 97 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">dbl</span> (117): AARP, AMA1, ASP, Buffer, CD4TAG, CLAG3.2, CommercialHumanIgG, EBA...</span> |
|
| 98 |
+<span class="r-msg co"><span class="r-pr">#></span> </span> |
|
| 99 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Use `spec()` to retrieve the full column specification for this data.</span> |
|
| 100 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Specify the column types or set `show_col_types = FALSE` to quiet this message.</span> |
|
| 101 |
+<span class="r-in"><span><span class="va">normlise_vsn</span> <span class="op"><-</span> <span class="fu"><a href="matrix_normalise.html">matrix_normalise</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">as.matrix</a></span><span class="op">(</span><span class="va">matrix_antigen</span><span class="op">)</span>,</span></span> |
|
| 102 |
+<span class="r-in"><span>method <span class="op">=</span> <span class="st">"vsn"</span>,</span></span> |
|
| 103 |
+<span class="r-in"><span>return_plot <span class="op">=</span> <span class="cn">FALSE</span></span></span> |
|
| 104 |
+<span class="r-in"><span><span class="op">)</span></span></span> |
|
| 105 |
+<span class="r-in"><span><span class="fu">plot_normalised</span><span class="op">(</span><span class="va">normlise_vsn</span>,method<span class="op">=</span><span class="st">"vsn"</span>,batch_correct<span class="op">=</span><span class="cn">FALSE</span><span class="op">)</span></span></span> |
|
| 106 |
+<span class="r-msg co"><span class="r-pr">#></span> `geom_smooth()` using method = 'loess' and formula = 'y ~ x'</span> |
|
| 107 |
+<span class="r-plt img"><img src="plot_normalised-1.png" alt="" width="700" height="433"></span> |
|
| 108 |
+</code></pre></div> |
|
| 109 |
+ </div> |
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+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |
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+ <div class="col-md-9 contents"> |
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+ <div class="page-header"> |
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+ <h1>Comparison of normalised data by feature</h1> |
|
| 57 |
+ <small class="dont-index">Source: <a href="https://github.com/Keniajin/protGear/blob/HEAD/R/normalisation_functions.R" class="external-link"><code>R/normalisation_functions.R</code></a></small> |
|
| 58 |
+ <div class="hidden name"><code>plot_normalised_antigen.Rd</code></div> |
|
| 59 |
+ </div> |
|
| 60 |
+ |
|
| 61 |
+ <div class="ref-description"> |
|
| 62 |
+ <p>Comparison of normalised data by feature</p> |
|
| 63 |
+ </div> |
|
| 64 |
+ |
|
| 65 |
+ <div id="ref-usage"> |
|
| 66 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">plot_normalised_antigen</span><span class="op">(</span><span class="va">exprs_normalised_df</span>, <span class="va">method</span>, <span class="va">batch_correct</span><span class="op">)</span></span></code></pre></div> |
|
| 67 |
+ </div> |
|
| 68 |
+ |
|
| 69 |
+ <div id="arguments"> |
|
| 70 |
+ <h2>Arguments</h2> |
|
| 71 |
+ <dl><dt>exprs_normalised_df</dt> |
|
| 72 |
+<dd><p>a normalised data frame</p></dd> |
|
| 73 |
+ |
|
| 74 |
+ |
|
| 75 |
+<dt>method</dt> |
|
| 76 |
+<dd><p>the method of normalisation used</p></dd> |
|
| 77 |
+ |
|
| 78 |
+ |
|
| 79 |
+<dt>batch_correct</dt> |
|
| 80 |
+<dd><p>the batch correction</p></dd> |
|
| 81 |
+ |
|
| 82 |
+</dl></div> |
|
| 83 |
+ <div id="value"> |
|
| 84 |
+ <h2>Value</h2> |
|
| 85 |
+ |
|
| 86 |
+ |
|
| 87 |
+<p>A ggplot of various normalisation approaches</p> |
|
| 88 |
+ </div> |
|
| 89 |
+ |
|
| 90 |
+ <div id="ref-examples"> |
|
| 91 |
+ <h2>Examples</h2> |
|
| 92 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">matrix_antigen</span> <span class="op"><-</span> <span class="fu">readr</span><span class="fu">::</span><span class="fu"><a href="https://readr.tidyverse.org/reference/read_delim.html" class="external-link">read_csv</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata"</span>, </span></span> |
|
| 93 |
+<span class="r-in"><span><span class="st">"matrix_antigen.csv"</span>, package<span class="op">=</span><span class="st">"protGear"</span><span class="op">)</span><span class="op">)</span></span></span> |
|
| 94 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="font-weight: bold;">Rows: </span><span style="color: #0000BB;">105</span> <span style="font-weight: bold;">Columns: </span><span style="color: #0000BB;">117</span></span> |
|
| 95 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Column specification</span> <span style="color: #00BBBB;">────────────────────────────────────────────────────────</span></span> |
|
| 96 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="font-weight: bold;">Delimiter:</span> ","</span> |
|
| 97 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">dbl</span> (117): AARP, AMA1, ASP, Buffer, CD4TAG, CLAG3.2, CommercialHumanIgG, EBA...</span> |
|
| 98 |
+<span class="r-msg co"><span class="r-pr">#></span> </span> |
|
| 99 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Use `spec()` to retrieve the full column specification for this data.</span> |
|
| 100 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Specify the column types or set `show_col_types = FALSE` to quiet this message.</span> |
|
| 101 |
+<span class="r-in"><span><span class="va">normlise_vsn</span> <span class="op"><-</span> <span class="fu"><a href="matrix_normalise.html">matrix_normalise</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">as.matrix</a></span><span class="op">(</span><span class="va">matrix_antigen</span><span class="op">)</span>,</span></span> |
|
| 102 |
+<span class="r-in"><span>method <span class="op">=</span> <span class="st">"vsn"</span>,</span></span> |
|
| 103 |
+<span class="r-in"><span>return_plot <span class="op">=</span> <span class="cn">FALSE</span></span></span> |
|
| 104 |
+<span class="r-in"><span><span class="op">)</span></span></span> |
|
| 105 |
+<span class="r-in"><span><span class="fu">plot_normalised_antigen</span><span class="op">(</span><span class="va">normlise_vsn</span>,method<span class="op">=</span><span class="st">"vsn"</span>,batch_correct<span class="op">=</span><span class="cn">FALSE</span><span class="op">)</span></span></span> |
|
| 106 |
+<span class="r-msg co"><span class="r-pr">#></span> `geom_smooth()` using method = 'loess' and formula = 'y ~ x'</span> |
|
| 107 |
+<span class="r-plt img"><img src="plot_normalised_antigen-1.png" alt="" width="700" height="433"></span> |
|
| 108 |
+</code></pre></div> |
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Read array files — read_array_files • protGear</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Read array files — read_array_files"><meta property="og:description" content="This helps to read the chip file(s)."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> |
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+ Articles |
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+ <span class="caret"></span> |
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+ </a> |
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+ <ul class="dropdown-menu" role="menu"><li> |
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+ <a href="../articles/vignette.html">protGear vignette processing suite</a> |
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+ </li> |
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+ </ul></li> |
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| 38 |
+<li> |
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| 39 |
+ <a href="../news/index.html">Changelog</a> |
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| 40 |
+</li> |
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| 41 |
+ </ul><ul class="nav navbar-nav navbar-right"><li> |
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+ <a href="https://github.com/Keniajin/protGear/" class="external-link"> |
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+ <span class="fab fa-github fa-lg"></span> |
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+ |
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+ </a> |
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+</li> |
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+ </ul></div><!--/.nav-collapse --> |
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+ </div><!--/.container --> |
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+</div><!--/.navbar --> |
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+ |
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+ |
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+ |
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+ </header><div class="row"> |
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| 54 |
+ <div class="col-md-9 contents"> |
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| 55 |
+ <div class="page-header"> |
|
| 56 |
+ <h1>Read array files</h1> |
|
| 57 |
+ <small class="dont-index">Source: <a href="https://github.com/Keniajin/protGear/blob/HEAD/R/read_files_functions.R" class="external-link"><code>R/read_files_functions.R</code></a></small> |
|
| 58 |
+ <div class="hidden name"><code>read_array_files.Rd</code></div> |
|
| 59 |
+ </div> |
|
| 60 |
+ |
|
| 61 |
+ <div class="ref-description"> |
|
| 62 |
+ <p>This helps to read the chip file(s).</p> |
|
| 63 |
+ </div> |
|
| 64 |
+ |
|
| 65 |
+ <div id="ref-usage"> |
|
| 66 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">read_array_files</span><span class="op">(</span><span class="va">i</span>, <span class="va">data_path</span>, <span class="va">genepix_vars</span><span class="op">)</span></span></code></pre></div> |
|
| 67 |
+ </div> |
|
| 68 |
+ |
|
| 69 |
+ <div id="arguments"> |
|
| 70 |
+ <h2>Arguments</h2> |
|
| 71 |
+ <dl><dt>i</dt> |
|
| 72 |
+<dd><p>The name of the file which the data are to be read from.</p></dd> |
|
| 73 |
+ |
|
| 74 |
+ |
|
| 75 |
+<dt>data_path</dt> |
|
| 76 |
+<dd><p>The path where the file with the data is located</p></dd> |
|
| 77 |
+ |
|
| 78 |
+ |
|
| 79 |
+<dt>genepix_vars</dt> |
|
| 80 |
+<dd><p>A list of specific definitions of the experiment design. |
|
| 81 |
+See <code><a href="array_vars.html">array_vars</a></code>.</p></dd> |
|
| 82 |
+ |
|
| 83 |
+</dl></div> |
|
| 84 |
+ <div id="value"> |
|
| 85 |
+ <h2>Value</h2> |
|
| 86 |
+ |
|
| 87 |
+ |
|
| 88 |
+<p>a number of data frames in the global environment</p> |
|
| 89 |
+ </div> |
|
| 90 |
+ <div id="details"> |
|
| 91 |
+ <h2>Details</h2> |
|
| 92 |
+ <p>Read multiple array files</p> |
|
| 93 |
+ </div> |
|
| 94 |
+ |
|
| 95 |
+ <div id="ref-examples"> |
|
| 96 |
+ <h2>Examples</h2> |
|
| 97 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co">## Not run:</span></span></span> |
|
| 98 |
+<span class="r-in"><span><span class="va">genepix_vars</span> <span class="op"><-</span> <span class="fu"><a href="array_vars.html">array_vars</a></span><span class="op">(</span></span></span> |
|
| 99 |
+<span class="r-in"><span>channel <span class="op">=</span> <span class="st">"635"</span>,</span></span> |
|
| 100 |
+<span class="r-in"><span>chip_path <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata"</span>, <span class="st">"array_data/machine1/"</span>, </span></span> |
|
| 101 |
+<span class="r-in"><span>package<span class="op">=</span><span class="st">"protGear"</span><span class="op">)</span>,</span></span> |
|
| 102 |
+<span class="r-in"><span>totsamples <span class="op">=</span> <span class="fl">21</span>,</span></span> |
|
| 103 |
+<span class="r-in"><span>blockspersample <span class="op">=</span> <span class="fl">2</span>,</span></span> |
|
| 104 |
+<span class="r-in"><span>mig_prefix <span class="op">=</span> <span class="st">"_first"</span>,</span></span> |
|
| 105 |
+<span class="r-in"><span>machine <span class="op">=</span> <span class="fl">1</span>,</span></span> |
|
| 106 |
+<span class="r-in"><span>date_process <span class="op">=</span> <span class="st">"0520"</span></span></span> |
|
| 107 |
+<span class="r-in"><span><span class="op">)</span></span></span> |
|
| 108 |
+<span class="r-in"><span><span class="va">file_read</span> <span class="op"><-</span> <span class="st">"KK2-06.txt"</span></span></span> |
|
| 109 |
+<span class="r-in"><span><span class="fu">read_array_files</span><span class="op">(</span>i<span class="op">=</span><span class="va">file_read</span>,</span></span> |
|
| 110 |
+<span class="r-in"><span>data_path<span class="op">=</span><span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata"</span>, <span class="st">"array_data/machine1/"</span>,</span></span> |
|
| 111 |
+<span class="r-in"><span>package<span class="op">=</span><span class="st">"protGear"</span><span class="op">)</span>, genepix_vars<span class="op">=</span><span class="va">genepix_vars</span><span class="op">)</span></span></span> |
|
| 112 |
+<span class="r-in"><span><span class="co">## End(Not run)</span></span></span> |
|
| 113 |
+</code></pre></div> |
|
| 114 |
+ </div> |
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| 115 |
+ </div> |
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+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |
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+ <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> |
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+ <p></p><p>Developed by Kennedy Mwai, James Mburu.</p> |
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+<div class="pkgdown"> |
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+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> |
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+ <a href="../articles/vignette.html">protGear vignette processing suite</a> |
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+ </ul></li> |
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+<li> |
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+ <a href="../news/index.html">Changelog</a> |
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+</li> |
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+ |
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+ |
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+ |
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+ |
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+ </header><div class="row"> |
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+ <div class="col-md-9 contents"> |
|
| 55 |
+ <div class="page-header"> |
|
| 56 |
+ <h1>Read a gpr file to visualize</h1> |
|
| 57 |
+ <small class="dont-index">Source: <a href="https://github.com/Keniajin/protGear/blob/HEAD/R/read_files_functions.R" class="external-link"><code>R/read_files_functions.R</code></a></small> |
|
| 58 |
+ <div class="hidden name"><code>read_array_visualize.Rd</code></div> |
|
| 59 |
+ </div> |
|
| 60 |
+ |
|
| 61 |
+ <div class="ref-description"> |
|
| 62 |
+ <p>Read a gpr file to visualize</p> |
|
| 63 |
+ </div> |
|
| 64 |
+ |
|
| 65 |
+ <div id="ref-usage"> |
|
| 66 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">read_array_visualize</span><span class="op">(</span><span class="va">infile</span><span class="op">)</span></span></code></pre></div> |
|
| 67 |
+ </div> |
|
| 68 |
+ |
|
| 69 |
+ <div id="arguments"> |
|
| 70 |
+ <h2>Arguments</h2> |
|
| 71 |
+ <dl><dt>infile</dt> |
|
| 72 |
+<dd><p>a .gpr file to be used to visualize the expression intensities |
|
| 73 |
+of the slide spots</p></dd> |
|
| 74 |
+ |
|
| 75 |
+</dl></div> |
|
| 76 |
+ <div id="value"> |
|
| 77 |
+ <h2>Value</h2> |
|
| 78 |
+ |
|
| 79 |
+ |
|
| 80 |
+<p>a data frame to visualize the background or foreground values</p> |
|
| 81 |
+ </div> |
|
| 82 |
+ |
|
| 83 |
+ <div id="ref-examples"> |
|
| 84 |
+ <h2>Examples</h2> |
|
| 85 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co">## Not run:</span></span></span> |
|
| 86 |
+<span class="r-in"><span><span class="fu">read_array_visualize</span><span class="op">(</span>infile <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata"</span>,</span></span> |
|
| 87 |
+<span class="r-in"><span><span class="st">"/array_data/machine1/KK2-06.txt"</span>, package<span class="op">=</span><span class="st">"protGear"</span><span class="op">)</span><span class="op">)</span></span></span> |
|
| 88 |
+<span class="r-out co"><span class="r-pr">#></span> Flags Normalize Autoflag Block Column Row Name ID X</span> |
|
| 89 |
+<span class="r-out co"><span class="r-pr">#></span> 1: 0 0 0 1 1 1 Landmark 1F1 2130</span> |
|
| 90 |
+<span class="r-out co"><span class="r-pr">#></span> 2: 0 0 0 1 2 1 MSP3.6 1B3 2360</span> |
|
| 91 |
+<span class="r-out co"><span class="r-pr">#></span> 3: 0 0 0 1 3 1 ETRAMP10.2 1H3 2590</span> |
|
| 92 |
+<span class="r-out co"><span class="r-pr">#></span> 4: 0 0 0 1 4 1 GAMA 1D5 2820</span> |
|
| 93 |
+<span class="r-out co"><span class="r-pr">#></span> 5: 0 0 0 1 5 1 MSRP4 1F5 3050</span> |
|
| 94 |
+<span class="r-out co"><span class="r-pr">#></span> --- </span> |
|
| 95 |
+<span class="r-out co"><span class="r-pr">#></span> 8060: 0 0 0 42 4 24 Buffer 1K12 18490</span> |
|
| 96 |
+<span class="r-out co"><span class="r-pr">#></span> 8061: 0 0 0 42 5 24 Buffer 1M12 18720</span> |
|
| 97 |
+<span class="r-out co"><span class="r-pr">#></span> 8062: 0 0 0 42 6 24 Buffer 1I8 18950</span> |
|
| 98 |
+<span class="r-out co"><span class="r-pr">#></span> 8063: 0 0 0 42 7 24 Commercial Human IgG 1O8 19180</span> |
|
| 99 |
+<span class="r-out co"><span class="r-pr">#></span> 8064: 0 0 0 42 8 24 Landmark 1K10 19410</span> |
|
| 100 |
+<span class="r-out co"><span class="r-pr">#></span> Y F635 Median B635 B635 Median SNR 635 F635 Median - B635 Index</span> |
|
| 101 |
+<span class="r-out co"><span class="r-pr">#></span> 1: 1150 65535 2443 2443 4.575 63092 1</span> |
|
| 102 |
+<span class="r-out co"><span class="r-pr">#></span> 2: 1150 5488 1126 1126 0.153 4362 2</span> |
|
| 103 |
+<span class="r-out co"><span class="r-pr">#></span> 3: 1150 6350 1026 1026 11.718 5324 3</span> |
|
| 104 |
+<span class="r-out co"><span class="r-pr">#></span> 4: 1150 15768 1059 1059 10.836 14709 4</span> |
|
| 105 |
+<span class="r-out co"><span class="r-pr">#></span> 5: 1150 65535 1413 1413 9.025 64122 5</span> |
|
| 106 |
+<span class="r-out co"><span class="r-pr">#></span> --- </span> |
|
| 107 |
+<span class="r-out co"><span class="r-pr">#></span> 8060: 60490 820 690 690 0.107 130 8060</span> |
|
| 108 |
+<span class="r-out co"><span class="r-pr">#></span> 8061: 60490 1168 737 737 0.423 431 8061</span> |
|
| 109 |
+<span class="r-out co"><span class="r-pr">#></span> 8062: 60490 2383 1125 1125 0.223 1258 8062</span> |
|
| 110 |
+<span class="r-out co"><span class="r-pr">#></span> 8063: 60490 65535 19685 19685 1.936 45850 8063</span> |
|
| 111 |
+<span class="r-out co"><span class="r-pr">#></span> 8064: 60490 65535 18134 18134 1.564 47401 8064</span> |
|
| 112 |
+<span class="r-in"><span><span class="co">## End(Not run)</span></span></span> |
|
| 113 |
+</code></pre></div> |
|
| 114 |
+ </div> |
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+ </div> |
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+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |
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+ <p></p><p>Developed by Kennedy Mwai, James Mburu.</p> |
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+ |
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+<div class="pkgdown"> |
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+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> |
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>RLM normalisation — rlm_normalise • protGear</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="RLM normalisation — rlm_normalise"><meta property="og:description" content="A function for method='rlm' from |
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+matrix_normalise."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> |
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+ <div class="col-md-9 contents"> |
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+ <div class="page-header"> |
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+ <h1>RLM normalisation</h1> |
|
| 58 |
+ <small class="dont-index">Source: <a href="https://github.com/Keniajin/protGear/blob/HEAD/R/normalisation_functions.R" class="external-link"><code>R/normalisation_functions.R</code></a></small> |
|
| 59 |
+ <div class="hidden name"><code>rlm_normalise.Rd</code></div> |
|
| 60 |
+ </div> |
|
| 61 |
+ |
|
| 62 |
+ <div class="ref-description"> |
|
| 63 |
+ <p>A function for <code>method='rlm'</code> from |
|
| 64 |
+<code><a href="matrix_normalise.html">matrix_normalise</a></code>.</p> |
|
| 65 |
+ </div> |
|
| 66 |
+ |
|
| 67 |
+ <div id="ref-usage"> |
|
| 68 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">rlm_normalise</span><span class="op">(</span><span class="va">rlm_normalise_df</span><span class="op">)</span></span></code></pre></div> |
|
| 69 |
+ </div> |
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+ |
|
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+ <div id="arguments"> |
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| 72 |
+ <h2>Arguments</h2> |
|
| 73 |
+ <dl><dt>rlm_normalise_df</dt> |
|
| 74 |
+<dd><p>rlm normalised data frame</p></dd> |
|
| 75 |
+ |
|
| 76 |
+</dl></div> |
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+ <div id="value"> |
|
| 78 |
+ <h2>Value</h2> |
|
| 79 |
+ |
|
| 80 |
+ |
|
| 81 |
+<p>an elist of RLM normalisation to be utilised by |
|
| 82 |
+<code><a href="rlm_normalise_matrix.html">rlm_normalise_matrix</a></code></p> |
|
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+ |
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+ |
|
| 85 |
+ </div> |
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+ |
|
| 87 |
+ <div id="ref-examples"> |
|
| 88 |
+ <h2>Examples</h2> |
|
| 89 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">matrix_antigen</span> <span class="op"><-</span> <span class="fu">readr</span><span class="fu">::</span><span class="fu"><a href="https://readr.tidyverse.org/reference/read_delim.html" class="external-link">read_csv</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata"</span>, </span></span> |
|
| 90 |
+<span class="r-in"><span><span class="st">"matrix_antigen.csv"</span>, package<span class="op">=</span><span class="st">"protGear"</span><span class="op">)</span><span class="op">)</span></span></span> |
|
| 91 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="font-weight: bold;">Rows: </span><span style="color: #0000BB;">105</span> <span style="font-weight: bold;">Columns: </span><span style="color: #0000BB;">117</span></span> |
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+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Column specification</span> <span style="color: #00BBBB;">────────────────────────────────────────────────────────</span></span> |
|
| 93 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="font-weight: bold;">Delimiter:</span> ","</span> |
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| 94 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">dbl</span> (117): AARP, AMA1, ASP, Buffer, CD4TAG, CLAG3.2, CommercialHumanIgG, EBA...</span> |
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| 95 |
+<span class="r-msg co"><span class="r-pr">#></span> </span> |
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| 96 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Use `spec()` to retrieve the full column specification for this data.</span> |
|
| 97 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Specify the column types or set `show_col_types = FALSE` to quiet this message.</span> |
|
| 98 |
+<span class="r-in"><span><span class="co">#rlm_normalise_df <- rlm_normalise_matrix(matrix_antigen=matrix_antigen, </span></span></span> |
|
| 99 |
+<span class="r-in"><span><span class="co">#array_matrix=array_matrix,</span></span></span> |
|
| 100 |
+<span class="r-in"><span><span class="co"># control_antigens=control_antigens)</span></span></span> |
|
| 101 |
+<span class="r-in"><span><span class="co"># rlm_normalise(rlm_normalise_df)</span></span></span> |
|
| 102 |
+</code></pre></div> |
|
| 103 |
+ </div> |
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+ </div> |
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+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |
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+ <p></p><p>Developed by Kennedy Mwai, James Mburu.</p> |
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new file mode 100644 |
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+<!DOCTYPE html> |
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Nomrmalise using RLM — rlm_normalise_matrix • protGear</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Nomrmalise using RLM — rlm_normalise_matrix"><meta property="og:description" content="A function for method='rlm' from |
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+matrix_normalise."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> |
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+<li> |
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+ <a href="../news/index.html">Changelog</a> |
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+</li> |
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+ </ul><ul class="nav navbar-nav navbar-right"><li> |
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+ <a href="https://github.com/Keniajin/protGear/" class="external-link"> |
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+ <span class="fab fa-github fa-lg"></span> |
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+ |
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+ </a> |
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+ </ul></div><!--/.nav-collapse --> |
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+ </div><!--/.container --> |
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+</div><!--/.navbar --> |
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+ |
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+ |
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+ |
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+ </header><div class="row"> |
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+ <div class="col-md-9 contents"> |
|
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+ <div class="page-header"> |
|
| 57 |
+ <h1>Nomrmalise using RLM</h1> |
|
| 58 |
+ <small class="dont-index">Source: <a href="https://github.com/Keniajin/protGear/blob/HEAD/R/normalisation_functions.R" class="external-link"><code>R/normalisation_functions.R</code></a></small> |
|
| 59 |
+ <div class="hidden name"><code>rlm_normalise_matrix.Rd</code></div> |
|
| 60 |
+ </div> |
|
| 61 |
+ |
|
| 62 |
+ <div class="ref-description"> |
|
| 63 |
+ <p>A function for <code>method='rlm'</code> from |
|
| 64 |
+<code><a href="matrix_normalise.html">matrix_normalise</a></code>.</p> |
|
| 65 |
+ </div> |
|
| 66 |
+ |
|
| 67 |
+ <div id="ref-usage"> |
|
| 68 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">rlm_normalise_matrix</span><span class="op">(</span><span class="va">matrix_antigen</span>, <span class="va">array_matrix</span>, <span class="va">control_antigens</span><span class="op">)</span></span></code></pre></div> |
|
| 69 |
+ </div> |
|
| 70 |
+ |
|
| 71 |
+ <div id="arguments"> |
|
| 72 |
+ <h2>Arguments</h2> |
|
| 73 |
+ <dl><dt>matrix_antigen</dt> |
|
| 74 |
+<dd><p>A matrix with antigen data</p></dd> |
|
| 75 |
+ |
|
| 76 |
+ |
|
| 77 |
+<dt>array_matrix</dt> |
|
| 78 |
+<dd><p>A matrix with control antigen data</p></dd> |
|
| 79 |
+ |
|
| 80 |
+ |
|
| 81 |
+<dt>control_antigens</dt> |
|
| 82 |
+<dd><p>the control antigens for RLM normalisation</p></dd> |
|
| 83 |
+ |
|
| 84 |
+</dl></div> |
|
| 85 |
+ <div id="value"> |
|
| 86 |
+ <h2>Value</h2> |
|
| 87 |
+ |
|
| 88 |
+ |
|
| 89 |
+<p>A RLM normalised data frame</p> |
|
| 90 |
+ </div> |
|
| 91 |
+ |
|
| 92 |
+ <div id="ref-examples"> |
|
| 93 |
+ <h2>Examples</h2> |
|
| 94 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">matrix_antigen</span> <span class="op"><-</span> <span class="fu">readr</span><span class="fu">::</span><span class="fu"><a href="https://readr.tidyverse.org/reference/read_delim.html" class="external-link">read_csv</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata"</span>,</span></span> |
|
| 95 |
+<span class="r-in"><span> <span class="st">"matrix_antigen.csv"</span>, package<span class="op">=</span><span class="st">"protGear"</span><span class="op">)</span><span class="op">)</span></span></span> |
|
| 96 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="font-weight: bold;">Rows: </span><span style="color: #0000BB;">105</span> <span style="font-weight: bold;">Columns: </span><span style="color: #0000BB;">117</span></span> |
|
| 97 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Column specification</span> <span style="color: #00BBBB;">────────────────────────────────────────────────────────</span></span> |
|
| 98 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="font-weight: bold;">Delimiter:</span> ","</span> |
|
| 99 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">dbl</span> (117): AARP, AMA1, ASP, Buffer, CD4TAG, CLAG3.2, CommercialHumanIgG, EBA...</span> |
|
| 100 |
+<span class="r-msg co"><span class="r-pr">#></span> </span> |
|
| 101 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Use `spec()` to retrieve the full column specification for this data.</span> |
|
| 102 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Specify the column types or set `show_col_types = FALSE` to quiet this message.</span> |
|
| 103 |
+<span class="r-in"><span><span class="co"># rlm_normalise_matrix(matrix_antigen=matrix_antigen,</span></span></span> |
|
| 104 |
+<span class="r-in"><span> <span class="co">#array_matrix=array_matrix,</span></span></span> |
|
| 105 |
+<span class="r-in"><span><span class="co"># control_antigens=control_antigens)</span></span></span> |
|
| 106 |
+</code></pre></div> |
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+ <div class="col-md-9 contents"> |
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+ <div class="page-header"> |
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| 56 |
+ <h1>tag_subtract</h1> |
|
| 57 |
+ <small class="dont-index">Source: <a href="https://github.com/Keniajin/protGear/blob/HEAD/R/cv_estimation_tag_functions.R" class="external-link"><code>R/cv_estimation_tag_functions.R</code></a></small> |
|
| 58 |
+ <div class="hidden name"><code>tag_subtract.Rd</code></div> |
|
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+ </div> |
|
| 60 |
+ |
|
| 61 |
+ <div class="ref-description"> |
|
| 62 |
+ <p>\\_End_Function_\\ #</p> |
|
| 63 |
+ </div> |
|
| 64 |
+ |
|
| 65 |
+ <div id="ref-usage"> |
|
| 66 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">tag_subtract</span><span class="op">(</span></span> |
|
| 67 |
+<span> <span class="va">dataC_mfi</span>,</span> |
|
| 68 |
+<span> <span class="va">tag_antigens</span>,</span> |
|
| 69 |
+<span> <span class="va">mean_best_CV_var</span>,</span> |
|
| 70 |
+<span> <span class="va">tag_file</span>,</span> |
|
| 71 |
+<span> <span class="va">batch_vars</span>,</span> |
|
| 72 |
+<span> sampleID_var <span class="op">=</span> <span class="st">"sampleID"</span>,</span> |
|
| 73 |
+<span> antigen_var <span class="op">=</span> <span class="st">"antigen"</span></span> |
|
| 74 |
+<span><span class="op">)</span></span></code></pre></div> |
|
| 75 |
+ </div> |
|
| 76 |
+ |
|
| 77 |
+ <div id="arguments"> |
|
| 78 |
+ <h2>Arguments</h2> |
|
| 79 |
+ <dl><dt>dataC_mfi</dt> |
|
| 80 |
+<dd><p>A dataframe</p></dd> |
|
| 81 |
+ |
|
| 82 |
+ |
|
| 83 |
+<dt>tag_antigens</dt> |
|
| 84 |
+<dd><p>A character vector with the names of proteins or antigens |
|
| 85 |
+used as TAG.</p></dd> |
|
| 86 |
+ |
|
| 87 |
+ |
|
| 88 |
+<dt>mean_best_CV_var</dt> |
|
| 89 |
+<dd><p>A character string containing the identifier of the |
|
| 90 |
+variable with the MFI values.</p></dd> |
|
| 91 |
+ |
|
| 92 |
+ |
|
| 93 |
+<dt>tag_file</dt> |
|
| 94 |
+<dd><p>A data frame with variables <code>antigen, TAG, TAG_name </code> |
|
| 95 |
+to show the TAG for the different antigens or proteins in dataC_mfi</p></dd> |
|
| 96 |
+ |
|
| 97 |
+ |
|
| 98 |
+<dt>batch_vars</dt> |
|
| 99 |
+<dd><p>A list of characters identifying variables in dataC_mfi |
|
| 100 |
+for indicating batch.</p></dd> |
|
| 101 |
+ |
|
| 102 |
+ |
|
| 103 |
+<dt>sampleID_var</dt> |
|
| 104 |
+<dd><p>A character string containing the name of the sample |
|
| 105 |
+identifier variable. Default set to 'sampleID'</p></dd> |
|
| 106 |
+ |
|
| 107 |
+ |
|
| 108 |
+<dt>antigen_var</dt> |
|
| 109 |
+<dd><p>A character string containing the name of the |
|
| 110 |
+features/protein variable. Default to 'antigen'</p></dd> |
|
| 111 |
+ |
|
| 112 |
+</dl></div> |
|
| 113 |
+ <div id="value"> |
|
| 114 |
+ <h2>Value</h2> |
|
| 115 |
+ |
|
| 116 |
+ |
|
| 117 |
+<p>A data frame of TAG values subtracted</p> |
|
| 118 |
+ </div> |
|
| 119 |
+ <div id="details"> |
|
| 120 |
+ <h2>Details</h2> |
|
| 121 |
+ <p>Subtract the purification TAG data</p> |
|
| 122 |
+ </div> |
|
| 123 |
+ |
|
| 124 |
+ <div id="ref-examples"> |
|
| 125 |
+ <h2>Examples</h2> |
|
| 126 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">tag_file</span> <span class="op"><-</span> <span class="fu">readr</span><span class="fu">::</span><span class="fu"><a href="https://readr.tidyverse.org/reference/read_delim.html" class="external-link">read_csv</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata"</span>, <span class="st">"TAG_antigens.csv"</span>, </span></span> |
|
| 127 |
+<span class="r-in"><span>package<span class="op">=</span><span class="st">"protGear"</span><span class="op">)</span><span class="op">)</span></span></span> |
|
| 128 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="font-weight: bold;">Rows: </span><span style="color: #0000BB;">126</span> <span style="font-weight: bold;">Columns: </span><span style="color: #0000BB;">3</span></span> |
|
| 129 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Column specification</span> <span style="color: #00BBBB;">────────────────────────────────────────────────────────</span></span> |
|
| 130 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="font-weight: bold;">Delimiter:</span> ","</span> |
|
| 131 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BB0000;">chr</span> (2): antigen, TAG_name</span> |
|
| 132 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">dbl</span> (1): TAG</span> |
|
| 133 |
+<span class="r-msg co"><span class="r-pr">#></span> </span> |
|
| 134 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Use `spec()` to retrieve the full column specification for this data.</span> |
|
| 135 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Specify the column types or set `show_col_types = FALSE` to quiet this message.</span> |
|
| 136 |
+<span class="r-in"><span><span class="va">tag_antigens</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"CD4TAG"</span>, <span class="st">"GST"</span>, <span class="st">"MBP"</span><span class="op">)</span></span></span> |
|
| 137 |
+<span class="r-in"><span><span class="va">batch_vars</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>machine <span class="op">=</span> <span class="st">"m1"</span>, day <span class="op">=</span> <span class="st">"0520"</span><span class="op">)</span></span></span> |
|
| 138 |
+<span class="r-in"><span><span class="va">dataC</span> <span class="op"><-</span> <span class="fu">readr</span><span class="fu">::</span><span class="fu"><a href="https://readr.tidyverse.org/reference/read_delim.html" class="external-link">read_csv</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata"</span>, <span class="st">"dataC.csv"</span>,</span></span> |
|
| 139 |
+<span class="r-in"><span> package<span class="op">=</span><span class="st">"protGear"</span><span class="op">)</span><span class="op">)</span></span></span> |
|
| 140 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="font-weight: bold;">Rows: </span><span style="color: #0000BB;">567</span> <span style="font-weight: bold;">Columns: </span><span style="color: #0000BB;">11</span></span> |
|
| 141 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Column specification</span> <span style="color: #00BBBB;">────────────────────────────────────────────────────────</span></span> |
|
| 142 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="font-weight: bold;">Delimiter:</span> ","</span> |
|
| 143 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #BB0000;">chr</span> (3): sampleID, antigen, iden</span> |
|
| 144 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BB00;">dbl</span> (8): sample_array_ID, FMedian, BGMedian, FMedianBG_correct, Block, Colum...</span> |
|
| 145 |
+<span class="r-msg co"><span class="r-pr">#></span> </span> |
|
| 146 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Use `spec()` to retrieve the full column specification for this data.</span> |
|
| 147 |
+<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> Specify the column types or set `show_col_types = FALSE` to quiet this message.</span> |
|
| 148 |
+<span class="r-in"><span><span class="co">## this file has 3 lab replicates and the default names</span></span></span> |
|
| 149 |
+<span class="r-in"><span><span class="va">dataCV</span> <span class="op"><-</span> <span class="fu"><a href="cv_estimation.html">cv_estimation</a></span><span class="op">(</span><span class="va">dataC</span> ,lab_replicates<span class="op">=</span><span class="fl">3</span><span class="op">)</span></span></span> |
|
| 150 |
+<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>The replicates are as expected per sample per antigen</span> |
|
| 151 |
+<span class="r-in"><span><span class="va">dataCV_best2</span> <span class="op"><-</span> <span class="fu"><a href="best_CV_estimation.html">best_CV_estimation</a></span><span class="op">(</span><span class="va">dataCV</span>,slide_id <span class="op">=</span> <span class="st">"iden"</span>, </span></span> |
|
| 152 |
+<span class="r-in"><span>lab_replicates <span class="op">=</span> <span class="fl">3</span>, cv_cut_off <span class="op">=</span> <span class="fl">20</span><span class="op">)</span></span></span> |
|
| 153 |
+<span class="r-msg co"><span class="r-pr">#></span> Adding missing grouping variables: `row`</span> |
|
| 154 |
+<span class="r-in"><span><span class="fu">tag_subtract</span><span class="op">(</span><span class="va">dataCV_best2</span>,tag_antigens<span class="op">=</span><span class="va">tag_antigens</span>, </span></span> |
|
| 155 |
+<span class="r-in"><span>mean_best_CV_var<span class="op">=</span><span class="st">"mean_best_CV"</span>,</span></span> |
|
| 156 |
+<span class="r-in"><span> tag_file <span class="op">=</span> <span class="va">tag_file</span>,antigen_var <span class="op">=</span> <span class="st">"antigen"</span>, batch_vars <span class="op">=</span> <span class="va">batch_vars</span><span class="op">)</span></span></span> |
|
| 157 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 126 × 35</span></span> |
|
| 158 |
+<span class="r-out co"><span class="r-pr">#></span> sampleID sample_ar…¹ TAG antigen meanX sdX sdX2_X3 sdX1_X3 sdX1_X2 CVX</span> |
|
| 159 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span> |
|
| 160 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 0.0085 11 0 AMA1 643. 98.5 70 69.3 139. 15.3 </span> |
|
| 161 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 0.0255 8 0 AMA1 699 52.6 74.2 33.9 40.3 7.52</span> |
|
| 162 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 0.076 5 0 AMA1 633. 81.3 35.4 77.1 112. 12.8 </span> |
|
| 163 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 0.23 2 0 AMA1 <span style="text-decoration: underline;">1</span>725. 60.5 32.5 84.8 52.3 3.51</span> |
|
| 164 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 0.73 19 0 AMA1 <span style="text-decoration: underline;">2</span>504. 119. 166. 61.5 105. 4.75</span> |
|
| 165 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 177.78 4 0 AMA1 <span style="text-decoration: underline;">58</span>262 709. 994. 383. 612. 1.22</span> |
|
| 166 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 19.75 10 0 AMA1 <span style="text-decoration: underline;">64</span>143. 353. 476. 367. 109. 0.55</span> |
|
| 167 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2.19 16 0 AMA1 <span style="text-decoration: underline;">9</span>243 383. 528. 156. 372. 4.15</span> |
|
| 168 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 533 1 0 AMA1 <span style="text-decoration: underline;">53</span>180. 559. 117. 735. 619. 1.05</span> |
|
| 169 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 59.26 7 0 AMA1 <span style="text-decoration: underline;">61</span>601 894. <span style="text-decoration: underline;">1</span>078. <span style="text-decoration: underline;">1</span>111. 32.5 1.45</span> |
|
| 170 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 116 more rows, 25 more variables: CVX2_X3 <dbl>, CVX1_X3 <dbl>,</span></span> |
|
| 171 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CVX1_X2 <dbl>, cvCat_all <chr>, cvSelected_all <dbl>, iden <chr>,</span></span> |
|
| 172 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># `1` <dbl>, `2` <dbl>, `3` <dbl>, x <chr>, meanX1_X2 <dbl>, meanX1_X3 <dbl>,</span></span> |
|
| 173 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># meanX2_X3 <dbl>, meanSelected <dbl>, mean_best_CV <dbl>, best_CV <dbl>,</span></span> |
|
| 174 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># best_CV_cat <chr>, TAG_name <chr>, CD4TAG <dbl>, GST <dbl>, MBP <dbl>,</span></span> |
|
| 175 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TAG_mfi <dbl>, mean_best_CV_tag <dbl>, machine <chr>, day <chr>, and</span></span> |
|
| 176 |
+<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># abbreviated variable name ¹sample_array_ID</span></span> |
|
| 177 |
+</code></pre></div> |
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| 178 |
+ </div> |
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+ </div> |
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+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |
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+ <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> |
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+ <div class="col-md-9 contents"> |
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+ <div class="page-header"> |
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+ <h1>Visualize the slide mimicking the original scan image.</h1> |
|
| 57 |
+ <small class="dont-index">Source: <a href="https://github.com/Keniajin/protGear/blob/HEAD/R/read_files_functions.R" class="external-link"><code>R/read_files_functions.R</code></a></small> |
|
| 58 |
+ <div class="hidden name"><code>visualize_slide.Rd</code></div> |
|
| 59 |
+ </div> |
|
| 60 |
+ |
|
| 61 |
+ <div class="ref-description"> |
|
| 62 |
+ <p>Visualize the slide mimicking the original scan image.</p> |
|
| 63 |
+ </div> |
|
| 64 |
+ |
|
| 65 |
+ <div id="ref-usage"> |
|
| 66 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">visualize_slide</span><span class="op">(</span><span class="va">infile</span>, <span class="va">MFI_var</span>, interactive <span class="op">=</span> <span class="cn">FALSE</span>, d_f <span class="op">=</span> <span class="cn">NA</span><span class="op">)</span></span></code></pre></div> |
|
| 67 |
+ </div> |
|
| 68 |
+ |
|
| 69 |
+ <div id="arguments"> |
|
| 70 |
+ <h2>Arguments</h2> |
|
| 71 |
+ <dl><dt>infile</dt> |
|
| 72 |
+<dd><p>a .gpr file to be used to visualize the expression |
|
| 73 |
+intensities of the slide spots</p></dd> |
|
| 74 |
+ |
|
| 75 |
+ |
|
| 76 |
+<dt>MFI_var</dt> |
|
| 77 |
+<dd><p>the MFI variable to plot, can be either the |
|
| 78 |
+background or foreground value</p></dd> |
|
| 79 |
+ |
|
| 80 |
+ |
|
| 81 |
+<dt>interactive</dt> |
|
| 82 |
+<dd><p>a logical to specify whether an interactive |
|
| 83 |
+graph is returned or not</p></dd> |
|
| 84 |
+ |
|
| 85 |
+ |
|
| 86 |
+<dt>d_f</dt> |
|
| 87 |
+<dd><p>a data frame with array data</p></dd> |
|
| 88 |
+ |
|
| 89 |
+</dl></div> |
|
| 90 |
+ <div id="value"> |
|
| 91 |
+ <h2>Value</h2> |
|
| 92 |
+ |
|
| 93 |
+ |
|
| 94 |
+<p>A ggplot of slide foreground values</p> |
|
| 95 |
+ </div> |
|
| 96 |
+ |
|
| 97 |
+ <div id="ref-examples"> |
|
| 98 |
+ <h2>Examples</h2> |
|
| 99 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co">## Not run:</span></span></span> |
|
| 100 |
+<span class="r-in"><span><span class="fu">visualize_slide</span><span class="op">(</span></span></span> |
|
| 101 |
+<span class="r-in"><span>infile <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata"</span>, <span class="st">"/array_data/machine1/KK2-06.txt"</span>,</span></span> |
|
| 102 |
+<span class="r-in"><span> package<span class="op">=</span><span class="st">"protGear"</span><span class="op">)</span>,</span></span> |
|
| 103 |
+<span class="r-in"><span>MFI_var <span class="op">=</span> <span class="st">"B635 Median"</span></span></span> |
|
| 104 |
+<span class="r-in"><span><span class="op">)</span></span></span> |
|
| 105 |
+<span class="r-plt img"><img src="visualize_slide-1.png" alt="" width="700" height="433"></span> |
|
| 106 |
+<span class="r-in"><span><span class="co">## End(Not run)</span></span></span> |
|
| 107 |
+</code></pre></div> |
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| 108 |
+ </div> |
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+ </div> |
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+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |
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+ <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> |
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+ </nav></div> |
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+ <p></p><p>Developed by Kennedy Mwai, James Mburu.</p> |
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|
| 57 |
+ <small class="dont-index">Source: <a href="https://github.com/Keniajin/protGear/blob/HEAD/R/read_files_functions.R" class="external-link"><code>R/read_files_functions.R</code></a></small> |
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+ <div class="hidden name"><code>visualize_slide_2d.Rd</code></div> |
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+ </div> |
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+ |
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+ <div class="ref-description"> |
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+ <p>Visualize the slide mimicking the original scan image using a 2d plot.</p> |
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| 63 |
+ </div> |
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+ |
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| 65 |
+ <div id="ref-usage"> |
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+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">visualize_slide_2d</span><span class="op">(</span><span class="va">infile</span>, <span class="va">MFI_var</span>, d_f <span class="op">=</span> <span class="cn">NA</span><span class="op">)</span></span></code></pre></div> |
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| 67 |
+ </div> |
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+ |
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+ <div id="arguments"> |
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+ <h2>Arguments</h2> |
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+ <dl><dt>infile</dt> |
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| 72 |
+<dd><p>- a .gpr file to be used to visualize the expression |
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+intensities of the slide spots</p></dd> |
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+ |
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+ |
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+<dt>MFI_var</dt> |
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+<dd><p>the MFI variable to plot, can be either the |
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+background or foreground value</p></dd> |
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+ |
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+ |
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+<dt>d_f</dt> |
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+<dd><p>a data frame with array data</p></dd> |
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+ |
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+</dl></div> |
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+ <div id="value"> |
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| 86 |
+ <h2>Value</h2> |
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+ |
|
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+ |
|
| 89 |
+<p>A 2d plot of either the background or foreground values</p> |
|
| 90 |
+ </div> |
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| 91 |
+ |
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| 92 |
+ <div id="ref-examples"> |
|
| 93 |
+ <h2>Examples</h2> |
|
| 94 |
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co">## Not run:</span></span></span> |
|
| 95 |
+<span class="r-in"><span><span class="fu">visualize_slide_2d</span><span class="op">(</span></span></span> |
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+<span class="r-in"><span>infile <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata"</span>, <span class="st">"/array_data/machine1/KK2-06.txt"</span>, </span></span> |
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| 97 |
+<span class="r-in"><span>package<span class="op">=</span><span class="st">"protGear"</span><span class="op">)</span>,</span></span> |
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| 98 |
+<span class="r-in"><span>MFI_var <span class="op">=</span> <span class="st">"B635 Median"</span></span></span> |
|
| 99 |
+<span class="r-in"><span><span class="op">)</span></span></span> |
|
| 100 |
+<span class="r-plt img"><img src="visualize_slide_2d-1.png" alt="" width="700" height="433"></span> |
|
| 101 |
+<span class="r-in"><span><span class="co">## End(Not run)</span></span></span> |
|
| 102 |
+</code></pre></div> |
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| 103 |
+ </div> |
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| 104 |
+ </div> |
|
| 105 |
+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |
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+ <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> |
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+ </nav></div> |
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+</div> |
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+ |
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+ |
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+ <footer><div class="copyright"> |
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| 112 |
+ <p></p><p>Developed by Kennedy Mwai, James Mburu.</p> |
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+</div> |
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+ |
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+<div class="pkgdown"> |
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| 116 |
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> |
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+</div> |
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+ |
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+ </footer></div> |
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+ </body></html> |
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