Browse code

resolv the bioc error?

Emanuel Soda authored on 13/05/2022 17:34:18
Showing11 changed files

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@@ -9,7 +9,7 @@ Authors@R: c(person("Emanuel Michele", "Soda", role = c("aut", "cre"),
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              person("Elena", "Ceccacci", role = c("aut"),
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                    email = "elena.ceccacci@ieo.it", 
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                    comment = c(ORICD = "0000-0002-2285-8994")))
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-Description:ScreenR is a package suitable to perform hit identification in loss 
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+Description: ScreenR is a package suitable to perform hit identification in loss 
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             of function High Throughput Biological Screenings performed using 
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             barcoded shRNA-based  libraries. ScreenR combines the computing 
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             power of software such as  edgeR with the simplicity of use of the 
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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>Create the table containing the Mapped Sample file — barcode_creation_dataframe • ScreenR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- 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="Create the table containing the Mapped Sample file — barcode_creation_dataframe"><meta property="og:description" content="This function takes as input the path of a list of files
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-             created using the Samtools idxstats tool and return a
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-              count table."><meta property="og:image" content="/logo.png"><!-- 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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-    <h1>Create the table containing the Mapped Sample file</h1>
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-    <small class="dont-index">Source: <a href="https://github.com/EmanuelSoda/ScreenR/blob/HEAD/R/barcode_creation_dataframe.R" class="external-link"><code>R/barcode_creation_dataframe.R</code></a></small>
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-    <div class="hidden name"><code>barcode_creation_dataframe.Rd</code></div>
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-    <div class="ref-description">
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-    <p>This function takes as input the path of a list of files
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-             created using the Samtools idxstats tool and return a
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-              count table.</p>
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-    </div>
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-    <div id="ref-usage">
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-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">barcode_creation_dataframe</span><span class="op">(</span><span class="va">path_file</span><span class="op">)</span></code></pre></div>
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-    </div>
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-    <div id="arguments">
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-    <h2>Arguments</h2>
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-    <dl><dt>path_file</dt>
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-<dd><p>Path of the list of files</p></dd>
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-</dl></div>
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-    <div id="value">
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-    <h2>Value</h2>
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-    <p>Return the table containing  the list of barcodes mapped in each of
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-        the samples (a count table).</p>
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-    </div>
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-  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci.</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>Create EdgeR Object — create_edger_obj • ScreenR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- 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="Create EdgeR Object — create_edger_obj"><meta property="og:description" content="Utility function that using the screenR-class
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-             object create the corresponding edgeR object"><meta property="og:image" content="/logo.png"><!-- 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="page-header">
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-    <h1>Create EdgeR Object</h1>
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-    <small class="dont-index">Source: <a href="https://github.com/EmanuelSoda/ScreenR/blob/HEAD/R/create_edger_obj.R" class="external-link"><code>R/create_edger_obj.R</code></a></small>
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-    <div class="hidden name"><code>create_edger_obj.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>Utility function that using the screenR-class
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-             object create the corresponding edgeR object</p>
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-    </div>
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-
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-    <div id="ref-usage">
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-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">create_edger_obj</span><span class="op">(</span><span class="va">screenR_Object</span><span class="op">)</span></code></pre></div>
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-    <h2>Arguments</h2>
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-    <dl><dt>screenR_Object</dt>
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-<dd><p>The ScreenR object obtained using the
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-<code><a href="create_screenr_object.html">create_screenr_object</a></code></p></dd>
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-</dl></div>
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-    <div id="value">
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-    <h2>Value</h2>
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-    <p>The edgeR object</p>
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-    <h2>Examples</h2>
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-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="va">object</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/exists.html" class="external-link">get0</a></span><span class="op">(</span><span class="st">"object"</span>, envir <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ns-internal.html" class="external-link">asNamespace</a></span><span class="op">(</span><span class="st">"ScreenR"</span><span class="op">)</span><span class="op">)</span></span>
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-<span class="r-in"><span class="fu">create_edger_obj</span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> An object of class "DGEList"</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> $counts</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span>          T1        T2 Time3_TRT_A Time3_TRT_B Time3_TRT_C   Time3_A   Time3_B</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> 1 329.84259 437.05313   365.28131   438.98590   310.56195 357.71537 424.65120</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> 2  26.23748  34.59281    20.51319    59.51235    16.67032  49.34005  17.41192</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> 3 141.21386 156.43298   164.10552   123.52655   132.33355 119.76559 121.43982</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> 4 355.79896 423.58336   336.41632   423.50391   375.08227 387.65676 346.46392</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> 5  67.18669  65.71614    82.63885    36.89326    26.34323  58.40681  65.43333</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span>     Time3_C Time4_TRT_A Time4_TRT_B Time4_TRT_C   Time4_A   Time4_B   Time4_c</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> 1 363.06161   323.48640   382.06214   456.79054 338.12714 358.16244 390.75227</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> 2  16.93033    32.46057    15.37962    33.91447  63.18147  29.41115  20.28906</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> 3 126.87300    14.21549    39.96678    50.70943  43.66670  41.17561  90.38830</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> 4 361.38947   259.79652   325.90629   280.80853 359.96049 338.11929 274.92213</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> 5  76.81355    35.70663    10.72526    32.53517  12.26918  43.89886  71.49478</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> 5315 more rows ...</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> $samples</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span>               group lib.size norm.factors</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> T1            T1/T2    1e+06            1</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> T2            T1/T2    1e+06            1</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> Time3_TRT_A Treated    1e+06            1</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> Time3_TRT_B Treated    1e+06            1</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> Time3_TRT_C Treated    1e+06            1</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> 9 more rows ...</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> $genes</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span>       Gene Barcode Gene_ID Sequence Library</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Gene_380   10208      NA       NA      NA</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> 2 Gene_380   10502      NA       NA      NA</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> 3 Gene_380   10796      NA       NA      NA</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> 4 Gene_380   11089      NA       NA      NA</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> 5 Gene_380   11382      NA       NA      NA</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> 5315 more rows ...</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
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-<span class="r-in"></span>
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-</code></pre></div>
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-    <h1>Create the ScreenR Object</h1>
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-    <small class="dont-index">Source: <a href="https://github.com/EmanuelSoda/ScreenR/blob/HEAD/R/create_screenr_object.R" class="external-link"><code>R/create_screenr_object.R</code></a></small>
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-    <div class="hidden name"><code>create_screenr_object.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>Initial function to create the Screen Object.</p>
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-    </div>
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-
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-    <div id="ref-usage">
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-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">create_screenr_object</span><span class="op">(</span>
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-  table <span class="op">=</span> <span class="cn">NULL</span>,
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-  annotation <span class="op">=</span> <span class="cn">NULL</span>,
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-  groups <span class="op">=</span> <span class="cn">NULL</span>,
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-  replicates <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">""</span><span class="op">)</span>
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-<span class="op">)</span></code></pre></div>
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-    </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>table</dt>
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-<dd><p>The count table obtained from the read alignment that
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-contains the Barcodes as rows and samples as columns.</p></dd>
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-<dt>annotation</dt>
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-<dd><p>The annotation table containing the information
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-for each Barcode and the association to the
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-corresponding Gene</p></dd>
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-<dt>groups</dt>
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-<dd><p>A factor containing the experimental design label</p></dd>
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-<dt>replicates</dt>
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-<dd><p>A vector containing the replicates label</p></dd>
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-</dl></div>
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-    <div id="value">
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-    <h2>Value</h2>
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-    <p>An object containing all the needed information for the analysis.</p>
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-    </div>
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-
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-    <div id="ref-examples">
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-    <h2>Examples</h2>
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-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="va">count_table</span> <span class="op">&lt;-</span></span>
96
-<span class="r-in">    <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>
97
-<span class="r-in">        Barcode <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">"Code_1"</span>, <span class="st">"Code_2"</span>, <span class="st">"Code_3"</span>, <span class="st">"Code_3"</span><span class="op">)</span>,</span>
98
-<span class="r-in">        Time_3_rep1 <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">"3520"</span>, <span class="st">"3020"</span>, <span class="st">"1507"</span>, <span class="st">"1400"</span><span class="op">)</span>,</span>
99
-<span class="r-in">        Time_3_rep2 <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">"3500"</span>, <span class="st">"3000"</span>, <span class="st">"1457"</span>, <span class="st">"1490"</span><span class="op">)</span>,</span>
100
-<span class="r-in">        Time_3_TRT_rep1 <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">"1200"</span>, <span class="st">"1100"</span>, <span class="st">"1300"</span>, <span class="st">"1350"</span><span class="op">)</span>,</span>
101
-<span class="r-in">        Time_3_TRT_rep2 <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">"1250"</span>, <span class="st">"1000"</span>, <span class="st">"1400"</span>, <span class="st">"1375"</span><span class="op">)</span></span>
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-<span class="r-in">    <span class="op">)</span></span>
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-<span class="r-in"><span class="va">annotation_table</span> <span class="op">&lt;-</span></span>
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-<span class="r-in">    <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>
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-<span class="r-in">        Gene <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">"Gene_1"</span>, <span class="st">"Gene_1"</span>, <span class="st">"Code_2"</span>, <span class="st">"Code_2"</span><span class="op">)</span>,</span>
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-<span class="r-in">        Barcode <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">"Code_1"</span>, <span class="st">"Code_2"</span>, <span class="st">"Code_3"</span>, <span class="st">"Code_3"</span><span class="op">)</span>,</span>
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-<span class="r-in">        Gene_ID <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="fl">4</span><span class="op">)</span>, Sequence <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="fl">4</span><span class="op">)</span>,</span>
108
-<span class="r-in">        Library <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="fl">4</span><span class="op">)</span></span>
109
-<span class="r-in">    <span class="op">)</span></span>
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-<span class="r-in"></span>
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-<span class="r-in"><span class="va">groups</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></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">"Control"</span>, <span class="st">"Control"</span>, <span class="st">"Treated"</span>, <span class="st">"Treated"</span><span class="op">)</span><span class="op">)</span></span>
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-<span class="r-in"><span class="va">obj</span> <span class="op">&lt;-</span> <span class="fu">create_screenr_object</span><span class="op">(</span></span>
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-<span class="r-in">    table <span class="op">=</span> <span class="va">count_table</span>,</span>
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-<span class="r-in">    annotation <span class="op">=</span> <span class="va">annotation_table</span>,</span>
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-<span class="r-in">    groups <span class="op">=</span> <span class="va">groups</span>, replicates <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">""</span><span class="op">)</span></span>
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-<span class="r-in"><span class="op">)</span></span>
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-<span class="r-in"><span class="va">obj</span></span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> An object of class "screenr_object"</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> Slot "count_table":</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 5</span></span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span>   Barcode Time_3_rep1 Time_3_rep2 Time_3_TRT_rep1 Time_3_TRT_rep2</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>       <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>       <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>           <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>          </span>
123
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Code_1  3520        3500        1200            1250           </span>
124
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Code_2  3020        3000        1100            1000           </span>
125
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Code_3  1507        1457        1300            1400           </span>
126
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> Code_3  1400        1490        1350            1375           </span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> Slot "annotation_table":</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 5</span></span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span>   Gene   Barcode Gene_ID Sequence Library</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;fct&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span>  </span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Gene_1 Code_1  <span style="color: #BB0000;">NA</span>      <span style="color: #BB0000;">NA</span>       <span style="color: #BB0000;">NA</span>     </span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Gene_1 Code_2  <span style="color: #BB0000;">NA</span>      <span style="color: #BB0000;">NA</span>       <span style="color: #BB0000;">NA</span>     </span>
134
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Code_2 Code_3  <span style="color: #BB0000;">NA</span>      <span style="color: #BB0000;">NA</span>       <span style="color: #BB0000;">NA</span>     </span>
135
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> Code_2 Code_3  <span style="color: #BB0000;">NA</span>      <span style="color: #BB0000;">NA</span>       <span style="color: #BB0000;">NA</span>     </span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
137
-<span class="r-out co"><span class="r-pr">#&gt;</span> Slot "groups":</span>
138
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] Control Control Treated Treated</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> Levels: Control Treated</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> Slot "replicates":</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ""</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
144
-<span class="r-out co"><span class="r-pr">#&gt;</span> Slot "normalized_count_table":</span>
145
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 0 × 0</span></span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
147
-<span class="r-out co"><span class="r-pr">#&gt;</span> Slot "data_table":</span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 0 × 0</span></span>
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-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
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-</code></pre></div>
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-    <h1>Multidimensional Scaling Plot</h1>
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-    <small class="dont-index">Source: <a href="https://github.com/EmanuelSoda/ScreenR/blob/HEAD/R/plot_mds.R" class="external-link"><code>R/plot_mds.R</code></a></small>
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-    <div class="hidden name"><code>plot_mds.Rd</code></div>
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-    <p>Plot samples on a two-dimensional scatterplot so that
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-             distances on the plot approximate the typical log2 fold
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-             changes between the samples.</p>
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-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">plot_mds</span><span class="op">(</span>
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-  <span class="va">screenR_Object</span>,
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-  groups <span class="op">=</span> <span class="cn">NULL</span>,
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-  alpha <span class="op">=</span> <span class="fl">0.8</span>,
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-  size <span class="op">=</span> <span class="fl">2.5</span>,
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-  color <span class="op">=</span> <span class="st">"black"</span>
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-<span class="op">)</span></code></pre></div>
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-    <h2>Arguments</h2>
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-    <dl><dt>screenR_Object</dt>
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-<dd><p>The Object of the package
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-<code><a href="create_screenr_object.html">create_screenr_object</a></code></p></dd>
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-<dt>groups</dt>
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-<dd><p>The vector that has to be used to fill the plot</p></dd>
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-<dt>alpha</dt>
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-<dd><p>The opacity of the labels</p></dd>
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-<dt>size</dt>
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-<dd><p>The dimension of the labels</p></dd>
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-<dt>color</dt>
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-<dd><p>The color of the labels</p></dd>
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-</dl></div>
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-    <div id="value">
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-    <h2>Value</h2>
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-    <p>The MDS Plot</p>
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-    <h2>Examples</h2>
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-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="va">object</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/exists.html" class="external-link">get0</a></span><span class="op">(</span><span class="st">"object"</span>, envir <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ns-internal.html" class="external-link">asNamespace</a></span><span class="op">(</span><span class="st">"ScreenR"</span><span class="op">)</span><span class="op">)</span></span>
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-<span class="r-in"></span>
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-<span class="r-in"><span class="fu">plot_mds</span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span>
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-<span class="r-plt img"><img src="plot_mds-1.png" alt="" width="700" height="433"></span>
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-</code></pre></div>
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3
-             Principal Component."><meta property="og:image" content="/logo.png"><!-- 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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-    <h1>Plot the explained variance by the PC</h1>
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-    <small class="dont-index">Source: <a href="https://github.com/EmanuelSoda/ScreenR/blob/HEAD/R/plot_mds.R" class="external-link"><code>R/plot_mds.R</code></a></small>
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-    <div class="hidden name"><code>plot_pc_explained_variance.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>This function plot the explained variance by the
64
-             Principal Component.</p>
65
-    </div>
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-
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-    <div id="ref-usage">
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-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">plot_pc_explained_variance</span><span class="op">(</span>
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-  <span class="va">screenR_Object</span>,
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-  cumulative <span class="op">=</span> <span class="cn">FALSE</span>,
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-  color <span class="op">=</span> <span class="st">"steelblue"</span>
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-<span class="op">)</span></code></pre></div>
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-    </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>screenR_Object</dt>
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-<dd><p>The ScreenR object</p></dd>
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-<dt>cumulative</dt>
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-<dd><p>A boolean value which indicates whether or not to plot
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-the cumulative variance</p></dd>
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-<dt>color</dt>
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-<dd><p>The color to fill the barplot</p></dd>
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-</dl></div>
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-    <div id="value">
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-    <h2>Value</h2>
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-    <p>The explained variance  plot</p>
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-    </div>
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-
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-    <div id="ref-examples">
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-    <h2>Examples</h2>
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-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="va">object</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/exists.html" class="external-link">get0</a></span><span class="op">(</span><span class="st">"object"</span>, envir <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ns-internal.html" class="external-link">asNamespace</a></span><span class="op">(</span><span class="st">"ScreenR"</span><span class="op">)</span><span class="op">)</span></span>
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-<span class="r-in"></span>
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-<span class="r-in"><span class="fu">plot_pc_explained_variance</span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span>
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-<span class="r-plt img"><img src="plot_pc_explained_variance-1.png" alt="" width="700" height="433"></span>
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-<span class="r-in"></span>
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-<span class="r-in"><span class="co"># For the cumulative plote</span></span>
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-<span class="r-in"><span class="fu">plot_pc_explained_variance</span><span class="op">(</span><span class="va">object</span>, cumulative <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
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-<span class="r-plt img"><img src="plot_pc_explained_variance-2.png" alt="" width="700" height="433"></span>
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-</code></pre></div>
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-             treated vs control in the different time points."><meta property="og:image" content="/logo.png"><!-- 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="page-header">
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-    <h1>Plot distribution Z-score</h1>
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-    <small class="dont-index">Source: <a href="https://github.com/EmanuelSoda/ScreenR/blob/HEAD/R/plot_zscore_distribution.R" class="external-link"><code>R/plot_zscore_distribution.R</code></a></small>
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-    <div class="hidden name"><code>plot_zscore_distribution.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>This function plots the Log2FC Z-score distribution of the
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-             treated vs control in the different time points.</p>
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-    </div>
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-
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-    <div id="ref-usage">
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-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">plot_zscore_distribution</span><span class="op">(</span><span class="va">time_point_measure</span>, alpha <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></code></pre></div>
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-    </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>time_point_measure</dt>
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-<dd><p>A list containing the table for each time
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-point. Each table contains for eaach barcode
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-the counts for the treated and control the Log2FC,
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-Zscore, ZscoreRobust, Day.</p></dd>
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-<dt>alpha</dt>
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-<dd><p>A value for the opacity of the plot.
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-Allowed values are in the range 0 to 1</p></dd>
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-</dl></div>
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-    <div id="value">
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-    <h2>Value</h2>
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-    <p>return the density plot of the distribution of the Z-score</p>
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-    </div>
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-
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-    <div id="ref-examples">
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-    <h2>Examples</h2>
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-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="va">object</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/exists.html" class="external-link">get0</a></span><span class="op">(</span><span class="st">"object"</span>, envir <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ns-internal.html" class="external-link">asNamespace</a></span><span class="op">(</span><span class="st">"ScreenR"</span><span class="op">)</span><span class="op">)</span></span>
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-<span class="r-in"></span>
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-<span class="r-in"><span class="va">table1</span> <span class="op">&lt;-</span> <span class="fu"><a href="compute_metrics.html">compute_metrics</a></span><span class="op">(</span><span class="va">object</span>,</span>
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-<span class="r-in">    control <span class="op">=</span> <span class="st">"TRT"</span>, treatment <span class="op">=</span> <span class="st">"Time3"</span>,</span>
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-<span class="r-in">    day <span class="op">=</span> <span class="st">"Time3"</span></span>
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-<span class="r-in"><span class="op">)</span></span>
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-<span class="r-in"></span>
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-<span class="r-in"><span class="va">table2</span> <span class="op">&lt;-</span> <span class="fu"><a href="compute_metrics.html">compute_metrics</a></span><span class="op">(</span><span class="va">object</span>,</span>
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-<span class="r-in">    control <span class="op">=</span> <span class="st">"TRT"</span>, treatment <span class="op">=</span> <span class="st">"Time4"</span>,</span>
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-<span class="r-in">    day <span class="op">=</span> <span class="st">"Time4"</span></span>
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-<span class="r-in"><span class="op">)</span></span>
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-<span class="r-in"></span>
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-<span class="r-in"><span class="fu">plot_zscore_distribution</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><span class="va">table1</span>, <span class="va">table2</span><span class="op">)</span>, alpha <span class="op">=</span> <span class="fl">0.5</span><span class="op">)</span></span>
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-<span class="r-plt img"><img src="plot_zscore_distribution-1.png" alt="" width="700" height="433"></span>
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-<span class="r-in"></span>
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-</code></pre></div>
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-  <p></p><p>Developed by Emanuel Michele Soda, Elena Ceccacci.</p>
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