diff --git a/DESCRIPTION b/DESCRIPTION index 21704d7..8a7d82b 100755 --- 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 Depends: R (>= 3.3.0), DESeq2 (>= 1.12.0), edgeR (>= 3.12.0), xtable diff --git a/NEWS b/NEWS index 28d2503..2676cd8 100755 --- 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 index 50e8ae3..e049c1d 100755 --- 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 index 4edd1d5..cbe10c6 100755 --- 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){