Browse code

Merge pull request #40 from HCBravoLab/deprecate

Creating naming schemes consistency and deprecating the load_* functions.

From: Joseph N. Paulson <jpaulson@jimmy.harvard.edu>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@121795 bc3139a8-67e5-0310-9ffc-ced21a209358

Hector Corrada Bravo authored on 05/10/2016 10:10:48
Showing17 changed files

... ...
@@ -64,6 +64,10 @@ load_biom,
64 64
 load_meta,
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 load_metaQ,
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 load_phenoData,
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+loadBiom,
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+loadMeta,
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+loadMetaQ,
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+loadPhenoData,
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 makeLabels,
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 mergeMRexperiments,
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 MRcoefs,
... ...
@@ -2,6 +2,7 @@ version 1.15.xx (2016)
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 	+ Added 'mergeMRexperiment' function
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 	+ Replaced RUnit with testthat library for unit testing
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 	+ Adding multiple upgrades and changes throughout
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+	+ Deprecated the load_* functions and created load* function.
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 version 1.13.xx (2015)
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 	+ Upgrade support for biom-format vs. 2.0
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 	+ Fixed issue - "MRtable, etc will report NA rows when user requests more features than available"
... ...
@@ -9,7 +9,7 @@
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 #' @param sl scaling factor for normalized counts.
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 #' @param qiimeVersion Format fData according to QIIME specifications (assumes only taxonomy in fData).
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 #' @return A biom object.
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-#' @seealso \code{\link{load_meta}} \code{\link{load_phenoData}} \code{\link{newMRexperiment}} \code{\link{load_biom}} \code{\link{biom2MRexperiment}}
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+#' @seealso \code{\link{loadMeta}} \code{\link{loadPhenoData}} \code{\link{newMRexperiment}} \code{\link{loadBiom}} \code{\link{biom2MRexperiment}}
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 MRexperiment2biom <- function(obj,id=NULL,norm=FALSE,log=FALSE,sl=1000,qiimeVersion=TRUE){
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     requireNamespace("biomformat")
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     id = id
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@@ -4,7 +4,7 @@
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 #' 
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 #' @param obj The biom object file.
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 #' @return A MRexperiment object.
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-#' @seealso \code{\link{load_meta}} \code{\link{load_phenoData}} \code{\link{newMRexperiment}} \code{\link{load_biom}}
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+#' @seealso \code{\link{loadMeta}} \code{\link{loadPhenoData}} \code{\link{newMRexperiment}} \code{\link{loadBiom}}
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 #' @examples
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 #' 
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 #' #library(biomformat)
... ...
@@ -13,7 +13,11 @@
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 #'  parameters to be passed to the modern version of the function (see table).
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 #' @docType package
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 #' @export fitMeta
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-#' @aliases deprecated_metagenomeSeq_function fitMeta
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+#' @aliases deprecated_metagenomeSeq_function fitMeta load_phenoData load_meta load_biom load_metaQ
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 #'
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 deprecated_metagenomeSeq_function <- function(x, value, ...){return(NULL)}
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 fitMeta <- function(...){.Deprecated("fitMeta",package="metagenomeSeq");return(fitLogNormal(...))}
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+load_phenoData <- function(...){.Deprecated("load_phenoData",package="metagenomeSeq");return(loadPhenodata(...))}
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+load_biom <- function(...){.Deprecated("load_biom",package="metagenomeSeq");return(loadBiom(...))}
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+load_meta <- function(...){.Deprecated("load_meta",package="metagenomeSeq");return(loadMeta(...))}
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+load_metaQ <- function(...){.Deprecated("load_metaQ",package="metagenomeSeq");return(loadMetaQ(...))}
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similarity index 69%
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rename from R/load_biom.R
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rename to R/loadBiom.R
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@@ -4,14 +4,14 @@
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 #' 
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 #' @param file The biom object filepath.
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 #' @return A MRexperiment object.
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-#' @seealso \code{\link{load_meta}} \code{\link{load_phenoData}} \code{\link{newMRexperiment}} \code{\link{biom2MRexperiment}}
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+#' @seealso \code{\link{loadMeta}} \code{\link{loadPhenoData}} \code{\link{newMRexperiment}} \code{\link{biom2MRexperiment}}
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 #' @examples
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 #' 
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 #' #library(biomformat)
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 #' #rich_dense_file = system.file("extdata", "rich_dense_otu_table.biom", package = "biomformat")
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-#' #x = load_biom(rich_dense_file)
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+#' #x = loadBiom(rich_dense_file)
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 #' #x
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-load_biom <- function(file){
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+loadBiom <- function(file){
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 	requireNamespace("biomformat")
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 	x = biomformat::read_biom(file);
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 	mrobj = biom2MRexperiment(x);
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similarity index 79%
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rename from R/load_meta.R
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rename to R/loadMeta.R
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@@ -3,17 +3,17 @@
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 #' Load a matrix of OTUs in a tab delimited format
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 #' 
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 #' 
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-#' @aliases load_meta metagenomicLoader
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+#' @aliases loadMeta metagenomicLoader
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 #' @param file Path and filename of the actual data file.
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 #' @param sep File delimiter.
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 #' @return A list with objects 'counts' and 'taxa'.
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-#' @seealso \code{\link{load_phenoData}}
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+#' @seealso \code{\link{loadPhenoData}}
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 #' @examples
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 #' 
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 #' dataDirectory <- system.file("extdata", package="metagenomeSeq")
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-#' lung = load_meta(file.path(dataDirectory,"CHK_NAME.otus.count.csv"))
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+#' lung = loadMeta(file.path(dataDirectory,"CHK_NAME.otus.count.csv"))
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 #' 
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-load_meta <- function(file,sep="\t")
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+loadMeta <- function(file,sep="\t")
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 {
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 	dat2 <- read.table(file,header=FALSE,sep=sep,nrows=1,stringsAsFactors=FALSE);
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 	subjects <- as.character(dat2[1,-1]);
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similarity index 86%
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rename from R/load_metaQ.R
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rename to R/loadMetaQ.R
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@@ -3,15 +3,15 @@
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 #' Load a matrix of OTUs in Qiime's format
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 #' 
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 #' 
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-#' @aliases load_metaQ qiimeLoader
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+#' @aliases loadMetaQ qiimeLoader
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 #' @param file Path and filename of the actual data file.
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 #' @return An list with 'counts' containing the count data, 'taxa' containing the otu annotation, and 'otus'.
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-#' @seealso \code{\link{load_meta}} \code{\link{load_phenoData}}
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+#' @seealso \code{\link{loadMeta}} \code{\link{loadPhenoData}}
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 #' @examples
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 #' 
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 #' # see vignette
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 #' 
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-load_metaQ <- function(file) {	
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+loadMetaQ <- function(file) {	
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 	dat2 <- read.delim(file,header=FALSE,stringsAsFactors=FALSE,nrows=1,skip=1);
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 	len = ncol(dat2)
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 	subjects = as.character(dat2[1,-c(1,len)]);
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similarity index 90%
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rename from R/load_phenoData.R
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rename to R/loadPhenoData.R
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@@ -3,18 +3,18 @@
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 #' Load a matrix of metadata associated with a study.
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 #' 
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 #' 
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-#' @aliases load_phenoData phenoData
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+#' @aliases loadPhenoData phenoData
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 #' @param file Path and filename of the actual clinical file.
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 #' @param tran Boolean. If the covariates are along the columns and samples
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 #' along the rows, then tran should equal TRUE.
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 #' @param sep The separator for the file.
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 #' @return The metadata as a dataframe.
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-#' @seealso \code{\link{load_meta}}
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+#' @seealso \code{\link{loadMeta}}
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 #' @examples
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 #' 
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 #' # see vignette
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 #' 
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-load_phenoData <-function(file,tran=TRUE,sep="\t")
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+loadPhenoData <-function(file,tran=TRUE,sep="\t")
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 {
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 	dat2 <- read.table(file,header=FALSE,sep=sep);
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... ...
@@ -27,6 +27,6 @@ A biom object.
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 Wrapper to convert MRexperiment objects to biom objects.
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 }
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 \seealso{
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-\code{\link{load_meta}} \code{\link{load_phenoData}} \code{\link{newMRexperiment}} \code{\link{load_biom}} \code{\link{biom2MRexperiment}}
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+\code{\link{loadMeta}} \code{\link{loadPhenoData}} \code{\link{newMRexperiment}} \code{\link{loadBiom}} \code{\link{biom2MRexperiment}}
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 }
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@@ -23,6 +23,6 @@ Wrapper to convert biom files to MRexperiment objects.
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 #biom2MRexperiment(x)
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 }
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 \seealso{
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-\code{\link{load_meta}} \code{\link{load_phenoData}} \code{\link{newMRexperiment}} \code{\link{load_biom}}
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+\code{\link{loadMeta}} \code{\link{loadPhenoData}} \code{\link{newMRexperiment}} \code{\link{loadBiom}}
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 }
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similarity index 61%
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rename from man/load_biom.Rd
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rename to man/loadBiom.Rd
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@@ -1,10 +1,10 @@
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 % Generated by roxygen2: do not edit by hand
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-% Please edit documentation in R/load_biom.R
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-\name{load_biom}
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-\alias{load_biom}
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+% Please edit documentation in R/loadBiom.R
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+\name{loadBiom}
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+\alias{loadBiom}
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 \title{Load objects organized in the Biom format.}
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 \usage{
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-load_biom(file)
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+loadBiom(file)
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 }
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 \arguments{
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 \item{file}{The biom object filepath.}
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@@ -19,10 +19,10 @@ Wrapper to load Biom formatted object.
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 #library(biomformat)
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 #rich_dense_file = system.file("extdata", "rich_dense_otu_table.biom", package = "biomformat")
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-#x = load_biom(rich_dense_file)
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+#x = loadBiom(rich_dense_file)
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 #x
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 }
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 \seealso{
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-\code{\link{load_meta}} \code{\link{load_phenoData}} \code{\link{newMRexperiment}} \code{\link{biom2MRexperiment}}
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+\code{\link{loadMeta}} \code{\link{loadPhenoData}} \code{\link{newMRexperiment}} \code{\link{biom2MRexperiment}}
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 }
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similarity index 68%
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rename from man/load_meta.Rd
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rename to man/loadMeta.Rd
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@@ -1,11 +1,11 @@
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 % Generated by roxygen2: do not edit by hand
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-% Please edit documentation in R/load_meta.R
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-\name{load_meta}
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-\alias{load_meta}
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+% Please edit documentation in R/loadMeta.R
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+\name{loadMeta}
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+\alias{loadMeta}
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 \alias{metagenomicLoader}
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 \title{Load a count dataset associated with a study.}
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 \usage{
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-load_meta(file, sep = "\\t")
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+loadMeta(file, sep = "\\t")
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 }
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 \arguments{
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 \item{file}{Path and filename of the actual data file.}
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@@ -21,10 +21,10 @@ Load a matrix of OTUs in a tab delimited format
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 \examples{
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 dataDirectory <- system.file("extdata", package="metagenomeSeq")
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-lung = load_meta(file.path(dataDirectory,"CHK_NAME.otus.count.csv"))
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+lung = loadMeta(file.path(dataDirectory,"CHK_NAME.otus.count.csv"))
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26 26
 }
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 \seealso{
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-\code{\link{load_phenoData}}
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+\code{\link{loadPhenoData}}
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 }
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similarity index 73%
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rename from man/load_metaQ.Rd
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rename to man/loadMetaQ.Rd
... ...
@@ -1,11 +1,11 @@
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 % Generated by roxygen2: do not edit by hand
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-% Please edit documentation in R/load_metaQ.R
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-\name{load_metaQ}
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-\alias{load_metaQ}
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+% Please edit documentation in R/loadMetaQ.R
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+\name{loadMetaQ}
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+\alias{loadMetaQ}
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 \alias{qiimeLoader}
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 \title{Load a count dataset associated with a study set up in a Qiime format.}
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 \usage{
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-load_metaQ(file)
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+loadMetaQ(file)
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 }
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 \arguments{
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 \item{file}{Path and filename of the actual data file.}
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@@ -22,6 +22,6 @@ Load a matrix of OTUs in Qiime's format
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 }
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 \seealso{
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-\code{\link{load_meta}} \code{\link{load_phenoData}}
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+\code{\link{loadMeta}} \code{\link{loadPhenoData}}
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 }
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similarity index 75%
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rename from man/load_phenoData.Rd
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rename to man/loadPhenoData.Rd
... ...
@@ -1,11 +1,11 @@
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 % Generated by roxygen2: do not edit by hand
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-% Please edit documentation in R/load_phenoData.R
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-\name{load_phenoData}
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-\alias{load_phenoData}
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+% Please edit documentation in R/loadPhenoData.R
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+\name{loadPhenoData}
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+\alias{loadPhenoData}
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 \alias{phenoData}
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 \title{Load a clinical/phenotypic dataset associated with a study.}
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 \usage{
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-load_phenoData(file, tran = TRUE, sep = "\\t")
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+loadPhenoData(file, tran = TRUE, sep = "\\t")
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 }
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 \arguments{
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 \item{file}{Path and filename of the actual clinical file.}
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@@ -27,6 +27,6 @@ Load a matrix of metadata associated with a study.
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 }
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 \seealso{
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-\code{\link{load_meta}}
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+\code{\link{loadMeta}}
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 }
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... ...
@@ -4,6 +4,10 @@
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 \name{metagenomeSeq-deprecated}
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 \alias{deprecated_metagenomeSeq_function}
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 \alias{fitMeta}
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+\alias{load_biom}
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+\alias{load_meta}
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+\alias{load_metaQ}
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+\alias{load_phenoData}
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 \alias{metagenomeSeq-deprecated}
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 \alias{metagenomeSeq-deprecated-package}
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 \title{Depcrecated functions in the metagenomeSeq package.}
... ...
@@ -82,22 +82,22 @@ Data is prepared and formatted as a \texttt{MRexperiment} object. For an overvie
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 \subsection{Biom-Format}
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-You can load in BIOM file format data, the output of many popular tools out there, using the \texttt{load$\_$biom} function. 
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+You can load in BIOM file format data, the output of many popular tools out there, using the \texttt{loadBiom} function. 
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 Tthe \texttt{biom2MRexperiment} and \texttt{MRexperiment2biom} functions serve as a gateway between the \texttt{biom-class} object defined in the \textbf{biom} package and a \texttt{MRexperiment-class} object.
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 \subsection{Loading count data}
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 Following preprocessing and annotation of sequencing data \texttt{metagenomeSeq} requires a count matrix with features along rows and samples along the columns.
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 \texttt{metagenomeSeq} includes functions for loading delimited files of counts 
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-\texttt{load$\_$meta} and phenodata \texttt{load$\_$phenoData}.
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+\texttt{loadMeta} and phenodata \texttt{loadPhenoData}.
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 As an example, a portion of the lung microbiome \cite{charlson} 
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 OTU matrix is provided in \texttt{metagenomeSeq}'s library "extdata" folder. 
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 The OTU matrix is stored as a tab delimited file.
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-\texttt{load\_meta} loads the taxa and counts into a list.
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+\texttt{loadMeta} loads the taxa and counts into a list.
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 <<loadData>>=
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 dataDirectory <- system.file("extdata", package="metagenomeSeq")
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-lung = load_meta(file.path(dataDirectory,"CHK_NAME.otus.count.csv")) 
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+lung = loadMeta(file.path(dataDirectory,"CHK_NAME.otus.count.csv")) 
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 dim(lung$counts)
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 @
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... ...
@@ -114,10 +114,10 @@ As our OTUs appear to be in order with the count matrix we loaded earlier, the n
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 \textbf{Warning}: features need to have the same names as the rows of the count matrix when we create the MRexperiment object for provenance purposes. 
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 \subsection{Loading metadata}
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-Phenotype data can be optionally loaded into \texttt{R} with \texttt{load\_phenoData}. This function loads the data as a list.
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+Phenotype data can be optionally loaded into \texttt{R} with \texttt{loadPhenoData}. This function loads the data as a list.
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 <<loadClin>>=
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-clin = load_phenoData(file.path(dataDirectory,"CHK_clinical.csv"),tran=TRUE)
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+clin = loadPhenoData(file.path(dataDirectory,"CHK_clinical.csv"),tran=TRUE)
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 ord = match(colnames(lung$counts),rownames(clin)) 
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 clin = clin[ord,]
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 head(clin[1:2,])