checkParameters

PF2-pasteur-fr · Aug 10, 2017 · 4101a8b · 4101a8b
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: SARTools
 Type: Package
 Title: Statistical Analysis of RNA-Seq Tools
 Version: 1.5.0
-Date: 2017-06-13
+Date: 2017-08-10
 Author: Marie-Agnes Dillies and Hugo Varet
 Maintainer: Hugo Varet <[email protected]>
 Depends: R (>= 3.3.0), DESeq2 (>= 1.12.0), edgeR (>= 3.12.0), xtable

diff --git a/NEWS b/NEWS
@@ -2,6 +2,7 @@ CHANGES IN VERSION 1.5.0
 ------------------------
 	o new HTML report (dynamic table of contents, automatic bibliography)
 	o simplified SERE calculations
+	o use of warning() instead of print() in checkParameters.edgeR() and checkParameters.DESeq2()
 
 CHANGES IN VERSION 1.4.1
 ------------------------

diff --git a/R/checkParameters.DESeq2.r b/R/checkParameters.DESeq2.r
@@ -25,80 +25,80 @@
 
 checkParameters.DESeq2 <- function(projectName,author,targetFile,rawDir,
                                    featuresToRemove,varInt,condRef,batch,fitType,
-								   cooksCutoff,independentFiltering,alpha,pAdjustMethod,
-								   typeTrans,locfunc,colors){
+                                   cooksCutoff,independentFiltering,alpha,pAdjustMethod,
+                                   typeTrans,locfunc,colors){
   problem <- FALSE
   if (!is.character(projectName) | length(projectName)!=1){
-    print("projectName must be a character vector of length 1")
-	problem <- TRUE
+    warning("projectName must be a character vector of length 1")
+    problem <- TRUE
   }
   if (!is.character(author) | length(author)!=1){
-    print("author must be a character vector of length 1")
-	problem <- TRUE
+    warning("author must be a character vector of length 1")
+    problem <- TRUE
   }
   if (!is.character(targetFile) | length(targetFile)!=1 || !file.exists(targetFile)){
-    print("targetFile must be a character vector of length 1 specifying an accessible file")
-	problem <- TRUE
+    warning("targetFile must be a character vector of length 1 specifying an accessible file")
+    problem <- TRUE
   }
   if (!is.character(rawDir) | length(rawDir)!=1 || is.na(file.info(rawDir)[1,"isdir"]) | !file.info(rawDir)[1,"isdir"]){
-    print("rawDir must be a character vector of length 1 specifying an accessible directory")
-	problem <- TRUE
+    warning("rawDir must be a character vector of length 1 specifying an accessible directory")
+    problem <- TRUE
   }
   if (!is.null(featuresToRemove) && !is.character(featuresToRemove)){
-    print("featuresToRemove must be a character vector or equal to NULL")
-	problem <- TRUE
+    warning("featuresToRemove must be a character vector or equal to NULL")
+    problem <- TRUE
   }
   if (!is.character(varInt) | length(varInt)!=1){
-    print("varInt must be a character vector of length 1")
-	problem <- TRUE
+    warning("varInt must be a character vector of length 1")
+    problem <- TRUE
   }
   if (!is.character(condRef) | length(condRef)!=1){
-    print("condRef must be a character vector of length 1")
-	problem <- TRUE
+    warning("condRef must be a character vector of length 1")
+    problem <- TRUE
   }
   if (!is.null(batch) && I(!is.character(batch) | length(batch)!=1)){
-    print("batch must be NULL or a character vector of length 1")
-	problem <- TRUE
+    warning("batch must be NULL or a character vector of length 1")
+    problem <- TRUE
   }
   if (!is.character(fitType) | length(fitType)!=1 || !I(fitType %in% c("parametric","local"))){
-    print("fitType must be equal to 'parametric' or 'local'")
-	problem <- TRUE
+    warning("fitType must be equal to 'parametric' or 'local'")
+    problem <- TRUE
   }
   if (!is.logical(cooksCutoff) | length(cooksCutoff)!=1){
-    print("cooksCutoff must be a boolean vector of length 1")
-	problem <- TRUE
+    warning("cooksCutoff must be a boolean vector of length 1")
+    problem <- TRUE
   }
   if (!is.logical(independentFiltering) | length(independentFiltering)!=1){
-    print("independentFiltering must be a boolean vector of length 1")
-	problem <- TRUE
+    warning("independentFiltering must be a boolean vector of length 1")
+    problem <- TRUE
   }
   if (!is.numeric(alpha) | length(alpha)!=1 || I(alpha<=0 | alpha>=1)){
-    print("alpha must be a numeric vector of length 1 with a value between 0 and 1")
-	problem <- TRUE
+    warning("alpha must be a numeric vector of length 1 with a value between 0 and 1")
+    problem <- TRUE
   }
   if (!is.character(pAdjustMethod) | length(pAdjustMethod)!=1 || !I(pAdjustMethod %in% p.adjust.methods)){
-    print(paste("pAdjustMethod must be a value in", paste(p.adjust.methods, collapse=", ")))
-	problem <- TRUE
+    warning(paste("pAdjustMethod must be a value in", paste(p.adjust.methods, collapse=", ")))
+    problem <- TRUE
   }
   if (!is.character(typeTrans) | length(typeTrans)!=1 || !I(typeTrans %in% c("VST","rlog"))){
-    print("typeTrans must be equal to 'VST' or 'rlog'")
-	problem <- TRUE
+    warning("typeTrans must be equal to 'VST' or 'rlog'")
+    problem <- TRUE
   }
   if (!is.character(locfunc) | length(locfunc)!=1 || !I(locfunc %in% c("median","shorth"))){
-    print("locfunc must be equal to 'median' or 'shorth'")
-	problem <- TRUE
+    warning("locfunc must be equal to 'median' or 'shorth'")
+    problem <- TRUE
   } else{
     if (locfunc=="shorth" & !I("genefilter" %in% installed.packages()[,"Package"])){
-	  print("Package genefilter is needed if using locfunc='shorth'")
-	  problem <- TRUE
-	}
+      warning("Package genefilter is needed if using locfunc='shorth'")
+      problem <- TRUE
+    }
   }
   areColors <- function(col){
     sapply(col, function(X){tryCatch(is.matrix(col2rgb(X)), error=function(e){FALSE})})
   }
   if (!is.vector(colors) || !all(areColors(colors))){
-    print("colors must be a vector of colors")
-	problem <- TRUE
+    warning("colors must be a vector of colors")
+    problem <- TRUE
   }
 
   if (!problem){

diff --git a/R/checkParameters.edgeR.r b/R/checkParameters.edgeR.r
@@ -23,67 +23,67 @@
 
 checkParameters.edgeR <- function(projectName,author,targetFile,rawDir,
                                   featuresToRemove,varInt,condRef,batch,alpha,
-								  pAdjustMethod,cpmCutoff,gene.selection,
-								  normalizationMethod,colors){
+                                  pAdjustMethod,cpmCutoff,gene.selection,
+                                  normalizationMethod,colors){
   problem <- FALSE
   if (!is.character(projectName) | length(projectName)!=1){
-    print("projectName must be a character vector of length 1")
-	problem <- TRUE
+    warning("projectName must be a character vector of length 1")
+    problem <- TRUE
   }
   if (!is.character(author) | length(author)!=1){
-    print("author must be a character vector of length 1")
-	problem <- TRUE
+    warning("author must be a character vector of length 1")
+    problem <- TRUE
   }
   if (!is.character(targetFile) | length(targetFile)!=1 || !file.exists(targetFile)){
-    print("targetFile must be a character vector of length 1 specifying an accessible file")
-	problem <- TRUE
+    warning("targetFile must be a character vector of length 1 specifying an accessible file")
+    problem <- TRUE
   }
   if (!is.character(rawDir) | length(rawDir)!=1 || is.na(file.info(rawDir)[1,"isdir"]) | !file.info(rawDir)[1,"isdir"]){
-    print("rawDir must be a character vector of length 1 specifying an accessible directory")
-	problem <- TRUE
+    warning("rawDir must be a character vector of length 1 specifying an accessible directory")
+    problem <- TRUE
   }  
   if (!is.null(featuresToRemove) && !is.character(featuresToRemove)){
-    print("featuresToRemove must be a character vector or equal to NULL")
-	problem <- TRUE
+    warning("featuresToRemove must be a character vector or equal to NULL")
+    problem <- TRUE
   }
   if (!is.character(varInt) | length(varInt)!=1){
-    print("varInt must be a character vector of length 1")
-	problem <- TRUE
+    warning("varInt must be a character vector of length 1")
+    problem <- TRUE
   }
   if (!is.character(condRef) | length(condRef)!=1){
-    print("condRef must be a character vector of length 1")
-	problem <- TRUE
+    warning("condRef must be a character vector of length 1")
+    problem <- TRUE
   }
   if (!is.null(batch) && I(!is.character(batch) | length(batch)!=1)){
-    print("batch must be NULL or a character vector of length 1")
-	problem <- TRUE
+    warning("batch must be NULL or a character vector of length 1")
+    problem <- TRUE
   }
   if (!is.numeric(alpha) | length(alpha)!=1 || I(alpha<=0 | alpha>=1)){
-    print("alpha must be a numeric vector of length 1 with a value between 0 and 1")
-	problem <- TRUE
+    warning("alpha must be a numeric vector of length 1 with a value between 0 and 1")
+    problem <- TRUE
   }
   if (!is.character(pAdjustMethod) | length(pAdjustMethod)!=1 || !I(pAdjustMethod %in% p.adjust.methods)){
-    print(paste("pAdjustMethod must be a value in", paste(p.adjust.methods, collapse=", ")))
-	problem <- TRUE
+    warning(paste("pAdjustMethod must be a value in", paste(p.adjust.methods, collapse=", ")))
+    problem <- TRUE
   }
   if (!is.numeric(cpmCutoff) | length(cpmCutoff)!=1 || cpmCutoff<0){
-    print("cpmCutoff must be a numeric vector of length 1 with a value equal to or greater than 0")
-	problem <- TRUE
+    warning("cpmCutoff must be a numeric vector of length 1 with a value equal to or greater than 0")
+    problem <- TRUE
   }
   if (!is.character(normalizationMethod) | length(normalizationMethod)!=1 || !I(normalizationMethod %in% c("TMM","RLE","upperquartile"))){
-    print("gene.selection must be equal to 'TMM', 'RLE' or 'upperquartile'")
-	problem <- TRUE
+    warning("gene.selection must be equal to 'TMM', 'RLE' or 'upperquartile'")
+    problem <- TRUE
   }
   if (!is.character(gene.selection) | length(gene.selection)!=1 || !I(gene.selection %in% c("pairwise","common"))){
-    print("gene.selection must be equal to 'pairwise' or 'common'")
-	problem <- TRUE
+    warning("gene.selection must be equal to 'pairwise' or 'common'")
+    problem <- TRUE
   }
   areColors <- function(col){
     sapply(col, function(X){tryCatch(is.matrix(col2rgb(X)), error=function(e){FALSE})})
   }
   if (!is.vector(colors) || !all(areColors(colors))){
-    print("colors must be a vector of colors")
-	problem <- TRUE
+    warning("colors must be a vector of colors")
+    problem <- TRUE
   }
 
   if (!problem){