refactored paste(..., sep="") to paste0(...)

R/02references.R

@@ -119,10 +119,10 @@ setMethod("buildRefDir", "EzRef", function(.Object, genomeFile, genesFile, genom
   genomeInfoList = cleanGenomeFiles(genomeFile, genesFile)
   writeXStringSet(genomeInfoList$genomeSeq, .Object@refFastaFile)
   ezWriteGff(genomeInfoList$gtf, .Object@refFeatureFile)
-  cmd = paste(paste("../../../", SAMTOOLS, sep=""), "faidx", .Object@refFastaFile)
+  cmd = paste0(paste("../../../", SAMTOOLS), "faidx", .Object@refFastaFile)
   ezSystem(cmd)
-  cmd = paste("java -jar", paste("../../../", file.path(PICARD_DIR, "picard-1.119.jar"), sep=""), "CreateSequenceDictionary",
-              paste("R=", .Object@refFastaFile, sep=""), paste("O=", sub(".fa$", ".dict", .Object@refFastaFile), sep=""))
+  cmd = paste0("java -jar", paste0("../../../", file.path(PICARD_DIR, "picard-1.119.jar")), "CreateSequenceDictionary",
+              paste0("R=", .Object@refFastaFile), paste("O=", sub(".fa$", ".dict", .Object@refFastaFile)))
   ezSystem(cmd)
   setwd(cd)
 })

R/03plotter.R

@@ -32,7 +32,7 @@ EzPlotter =
                   if (ezIsSpecified(file)) {
                     filename = file
                   } else {
-                    filename = paste(name, ".png", sep="")
+                    filename = paste0(name, ".png")
                   }
 
                   if (!inherits(plotWidth, "uninitializedField")){
@@ -53,7 +53,7 @@ EzPlotter =
                   if (ezIsSpecified(file)) {
                     filename = file
                   } else {
-                    filename = paste(name, ".pdf", sep="")
+                    filename = paste0(name, ".pdf")
                   }
 
                   if (!inherits(plotWidth, "uninitializedField")){

R/app-BamPreview.R

@@ -20,8 +20,8 @@ ezMethodBamPreview = function(input=NA, output=NA, param=NA, htmlFile="00index.h
   }
 
   bamMeta = input$meta[ , !input$columnHasTag("File")]
-  bamMeta[["BAM [File]"]] = paste(cwd, "/", input$getNames(), "/", input$getNames(), ".bam", sep="")
-  bamMeta[["BAI [File]"]] = paste(cwd, "/", input$getNames(), "/", input$getNames(), ".bam.bai", sep="")
+  bamMeta[["BAM [File]"]] = paste0(cwd, "/", input$getNames(), "/", input$getNames(), ".bam")
+  bamMeta[["BAI [File]"]] = paste0(cwd, "/", input$getNames(), "/", input$getNames(), ".bam.bai")
   bamMeta[["Read Count"]] = round(bamMeta[["Read Count"]] / param$subsampleReads)
   bamOutput = EzDataset(meta=bamMeta)
   bamParam = param

R/app-RnaBamStats.R

@@ -135,7 +135,7 @@ getPosErrorFromBam = function(bamFile, param){
   chromSel = names(seqLengths)[which.max(seqCounts)]
 
   result = list()
-  chromFn = file.path(param$ezRef["refChromDir"], paste(chromSel, ".fa", sep=""))
+  chromFn = file.path(param$ezRef["refChromDir"], paste0(chromSel, ".fa"))
   stopifnot(!is.null(chromFn))
   targetGenome = readDNAStringSet(chromFn)[[1]]
   ezWriteElapsed(job, "read reference genome done")
@@ -218,7 +218,7 @@ getStatsFromBamParallel = function(seqLengths, param, bamFile, sm, nReads, gff=N
   chromResults = ezMclapply(seqNames, getStatsFromBamSingleChrom, param, bamFile, sm, nReads, gff, repeatsGff,
                              mc.preschedule=FALSE, mc.cores=ezThreads())
   if (param$saveImage){
-    save(chromResults, file=paste(sm, "-chromResults.RData", sep=""))
+    save(chromResults, file=paste0(sm, "-chromResults.RData"))
   }
   gc()
   result = list()
@@ -576,7 +576,7 @@ ezPosSpecErrorRate = function(bam, ReferenceGenome, nMaxReads=100000){
   noOfS = as.integer(sub("S", "", clipCigar))
   noOfS[is.na(noOfS)] = 0
   nEndClipped = noOfH + noOfS
-  bam$seq = paste(Xbegin, bam$seq, Xend, sep="")
+  bam$seq = paste0(Xbegin, bam$seq, Xend)
 
   seqChar = strsplit(as.character(bam$seq),"")
   readLength = sapply(seqChar, length)
@@ -622,12 +622,12 @@ ezPosSpecErrorRate = function(bam, ReferenceGenome, nMaxReads=100000){
 getJunctionPlotsFromBam = function(bamFile, param){
   pngFiles = list()
   ## do the junction annotation
-  outputJunction = paste("junction-", Sys.getpid(),sep="")
+  outputJunction = paste0("junction-", Sys.getpid())
   bed = getReferenceFeaturesBed(param)
   stopifnot(!is.null(bed))
   cmd = paste(JUNCTION_ANNOTATION, "--mapq=1", "-i", bamFile, "-o", outputJunction, "-r", bed)
   res = ezSystem(cmd, stopOnFailure=FALSE)
-  junctionFile = paste(outputJunction, ".junction.xls", sep="")
+  junctionFile = paste0(outputJunction, ".junction.xls")
   if (res == 0 && length(readLines(junctionFile)) > 1){
     juncsTable = read.table(junctionFile, header=TRUE)
     junctions = table(juncsTable$annotation) / length(juncsTable$annotation) *100
@@ -664,7 +664,7 @@ getJunctionPlotsFromBam = function(bamFile, param){
   }
 
   ## do the cleaning
-  file.remove(list.files(path=".", pattern=paste(outputJunction, ".+", sep="")))
+  file.remove(list.files(path=".", pattern=paste0(outputJunction, ".+")))
   return(pngFiles)
 }
 

R/app-chipStats.R

@@ -127,8 +127,8 @@ EzAppChipStats <-
 
 galp2gal = function(galp){ 
   system('echo Function galp2gal, conversion of paired-end data into single end data... \n')
-  betweenPairCigar = paste(abs(start(right(galp)) - end(left(galp)) + 1), "N", sep="")
-  galcigar = paste(cigar(left(galp)), betweenPairCigar, cigar(right(galp)), sep="")
+  betweenPairCigar = paste0(abs(start(right(galp)) - end(left(galp)) + 1), "N")
+  galcigar = paste0(cigar(left(galp)), betweenPairCigar, cigar(right(galp)))
   gal = GAlignments(
     seqnames = seqnames(galp),
     pos = start(left(galp)),
@@ -181,7 +181,7 @@ fragmentSize = function(myBam, isPaired = F){
     system('echo sample_fragmentSize calculated, plotting... \n')
     png(file=paste(names(myBam),"_fragmentSize.png",sep=''))
     d = density(sample_fragmentSize)
-    plot(d, main=names(myBam),xlab=paste("Median of FragmentSize:",medianFS,sep=""))
+    plot(d, main=names(myBam),xlab=paste0("Median of FragmentSize:",medianFS))
     polygon(d, col="red", border="black") 
     legend("topright",c(names(myBam)))
     dev.off()
@@ -357,7 +357,7 @@ binMyBam = function(cov, binLength, sampleName){
       MyBins = c(MyBins,rep(runValue(cov[[i]]),runLength(cov[[i]])))
     }
   }
-  write.table(MyBins,paste(sampleName,'_',binLength,'_BinData.txt',sep=""),col.names=F,quote=F,sep='\t')
+  write.table(MyBins,paste0(sampleName,'_',binLength,'_BinData.txt'),col.names=F,quote=F,sep='\t')
 }
 
 clusterData = function(data, distmethod='pearson', clustermethod='ward', title = title){

R/app-countQC.R

@@ -116,11 +116,11 @@ runNgsCountQC = function(dataset, htmlFile="00index.html", param=param, rawData=
     if (!is.null(seqAnno)){
       combined = cbind(seqAnno[rownames(combined), ,drop=FALSE], combined)
     }
-    countFile = paste(ezValidFilename(param$name), "-raw-count.txt", sep="")
+    countFile = paste0(ezValidFilename(param$name), "-raw-count.txt")
     ezWrite.table(rawData$counts, file=countFile, head="Feature ID", digits=4)
-    signalFile = paste(ezValidFilename(param$name), "-normalized-signal.txt", sep="")
+    signalFile = paste0(ezValidFilename(param$name), "-normalized-signal.txt")
     ezWrite.table(combined, file=signalFile, head="Feature ID", digits=4)
-    rpkmFile = paste(ezValidFilename(param$name), "-rpkm.txt", sep="")
+    rpkmFile = paste0(ezValidFilename(param$name), "-rpkm.txt")
     ezWrite.table(getRpkm(rawData), file=rpkmFile, head="Feature ID", digits=4)
     if (param$doZip){
       dataFiles =c(zipFile(countFile), zipFile(signalFile), zipFile(rpkmFile))
@@ -163,22 +163,22 @@ runNgsCountQC = function(dataset, htmlFile="00index.html", param=param, rawData=
 
   pngName = "sampleCorrelation-AllPresent.png"
   try({ezCorrelationPlot(png=pngName, cor(x, use="complete.obs"), cond=conds, condLabels=conds, 
-    main=paste("all present genes (", sum(isValid), ")", sep=""), sampleColors=sampleColors)})
+    main=paste0("all present genes (", sum(isValid), ")"), sampleColors=sampleColors)})
   pngNames[1, 1] = pngName
 
   pngName = "sampleCorrelation-AllPresentNormalized.png"
   try({ezCorrelationPlot(png=pngName, cor(xNormed, use="complete.obs"), cond=conds, condLabels=conds, 
-                         main=paste("all present genes (", sum(isValid), ") gene-wise normalized", sep=""))})
+                         main=paste0("all present genes (", sum(isValid), ") gene-wise normalized"))})
   pngNames[1,2] = pngName
 
   pngName = "sampleCorrelation-TopGenes.png"
   try({ezCorrelationPlot(png=pngName, cor(x[topGenes,], use="complete.obs"), cond=conds, condLabels=conds, 
-                         main=paste("top genes (", length(topGenes), ")", sep=""))})
+                         main=paste0("top genes (", length(topGenes), ")"))})
   pngNames[2,1] = pngName
 
   pngName = "sampleCorrelation-TopGenesNormalized.png"
   try({ezCorrelationPlot(png=pngName, cor(xNormed[topGenes,], use="complete.obs"), cond=conds, condLabels=conds, 
-                         main=paste("top genes (", length(topGenes), ") gene-wise normalized", sep=""))})
+                         main=paste0("top genes (", length(topGenes), ") gene-wise normalized"))})
   pngNames[2,2] = pngName
 
   ezWrite("<h2>Sample correlation</h2>", con=html)

R/app-edgerTwoGroups.R

@@ -363,7 +363,7 @@ runGfold = function(rawData, scalingFactors, isSample, isRef){
     if (is.null(gene_name)) gene_name = "NA"
     gfoldData = data.frame(gene_name=gene_name, count=rawData$counts[, sampleName], rawData$seqAnno$width, 
                            rawData$rpkm[, sampleName], row.names=rownames(rawData$seqAnno), check.names=FALSE, stringsAsFactors=FALSE)
-    gfoldFile = paste(sampleName, ".read_cnt", sep="")
+    gfoldFile = paste0(sampleName, ".read_cnt")
     ezWrite.table(gfoldData, file=gfoldFile, col.names = FALSE)
     return(gfoldFile)
   }

R/app-fastQC.R

@@ -18,9 +18,9 @@ ezMethodFastQC = function(input=NA, output=NA, param=NA, htmlFile="00index.html"
   samples = rownames(dataset)
   files = c()
   for (sm in samples){
-    files[paste(sm, "_R1", sep="")] = input$getFullPaths(param,"Read1")[sm]
+    files[paste0(sm, "_R1")] = input$getFullPaths(param,"Read1")[sm]
     if (!is.null(dataset$Read2)){
-      files[paste(sm, "_R2", sep="")] = input$getFullPaths(param,"Read2")[sm]    
+      files[paste0(sm, "_R2")] = input$getFullPaths(param,"Read2")[sm]    
     }
   }
   nFiles = length(files)
@@ -53,7 +53,7 @@ ezMethodFastQC = function(input=NA, output=NA, param=NA, htmlFile="00index.html"
   plotPages = sub(".png", ".html", plots)
   for (i in 1:length(plots)){
     plotHtml = openBsdocReport(title=paste("FASTQC:", plotPages[i]))
-    png = paste("<img src=", reportDir, "/Images/", plots[i], ">", sep="")
+    png = paste0("<img src=", reportDir, "/Images/", plots[i], ">")
     tbl = ezMatrix(png, rows=names(files), cols=names(plots)[i])
     plotHtml = addTableToReport(tbl, plotHtml)
     closeBsdocReport(plotHtml, plotPages[i])
@@ -81,15 +81,15 @@ ezMethodFastQC = function(input=NA, output=NA, param=NA, htmlFile="00index.html"
   for (i in 1:nFiles){
     smy = ezRead.table(file.path(reportDir[i], "summary.txt"), row.names=NULL, header=FALSE)
     if (i == 1){
-      rowNames = paste("<a href=", reportDir, "/fastqc_report.html>", names(files), "</a>", sep="")
+      rowNames = paste0("<a href=", reportDir, "/fastqc_report.html>", names(files), "</a>")
       colNames = ifelse(smy[[2]] %in% names(plotPages),
-                        paste("<a href=", plotPages[smy[[2]]], ">", smy[[2]], "</a>", sep=""),
+                        paste0("<a href=", plotPages[smy[[2]]], ">", smy[[2]], "</a>"),
                         smy[[2]])
       tbl = ezMatrix("", rows=rowNames, cols=colNames)
     }
-    href = paste(reportDir[i], "/fastqc_report.html#M", 0:(ncol(tbl)-1), sep="")
-    img = paste(reportDir[i], 	"/Icons/", statusToPng[smy[[1]]], sep="")
-    tbl[i, ] = paste("<a href=", href, "><img src=", img, "></a>", sep="")
+    href = paste0(reportDir[i], "/fastqc_report.html#M", 0:(ncol(tbl)-1))
+    img = paste0(reportDir[i], 	"/Icons/", statusToPng[smy[[1]]])
+    tbl[i, ] = paste0("<a href=", href, "><img src=", img, "></a>")
   }
   html = addTableToReport(tbl, html)
 
@@ -119,7 +119,7 @@ ezMethodFastQC = function(input=NA, output=NA, param=NA, htmlFile="00index.html"
   ezSessionInfo()
   html = addParagraph(html, pot("sessionInfo.txt", hyperlink = "sessionInfo.txt"))
   closeBsdocReport(html, htmlFile)
-  ezSystem(paste("rm -rf ", paste(reportDir, ".zip", sep="", collapse=" ")))
+  ezSystem(paste("rm -rf ", paste0(reportDir, ".zip", collapse=" ")))
   return("Success")
 }
 
@@ -229,7 +229,7 @@ plotQualityMatrixAsHeatmap = function(qualMatrixList, isR2=FALSE, xScale=1, ySca
   for(nm in names(index)){
     idx = index[[nm]]
     ## Plot the color key for the average quality heatmap R1_1
-    colorKeyFile = paste("averageReadsQuality-Key_", nm, ".png", sep="")
+    colorKeyFile = paste0("averageReadsQuality-Key_", nm, ".png")
     by.label = 1
     at=seq(from=minPercent, to=maxPercent, by=by.label)
     ezColorLegend(file=colorKeyFile, colorRange=c(minPercent, maxPercent), 
@@ -255,13 +255,13 @@ plotQualityMatrixAsHeatmap = function(qualMatrixList, isR2=FALSE, xScale=1, ySca
     result = result / resultCount
     avgQual = signif(prop.table(result,2) * 100, digits=3)
     pngFileName = plotQualityHeatmap(sqrt(avgQual), colorRange=c(minPercent, maxPercent), 
-                                     pngFileName=paste("averageReadsQuality-heatmap_", nm, ".png", sep=""),
+                                     pngFileName=paste0("averageReadsQuality-heatmap_", nm, ".png"),
                                      colors=colorsGray, main=paste("averageReadsQuality", nm, sep="_"), 
                                      xScale=xScale, yScale=yScale)
     pngTable["Average", nm] = pngFileName
 
     ## plot the difference quality heatmap for R1_1
-    colorKeyFile = paste("diffReadsQuality-Key_", nm, ".png", sep="")
+    colorKeyFile = paste0("diffReadsQuality-Key_", nm, ".png")
     at=seq(from=minDiff, to=maxDiff, by=by.label)
     ezColorLegend(file=colorKeyFile, colorRange=c(minDiff, maxDiff), colors=ezRedBlueScale(256),
                   vertical=FALSE, height=200*xScale, width=400*yScale, by.label=by.label, at=at, labels=as.character(at))
@@ -270,7 +270,7 @@ plotQualityMatrixAsHeatmap = function(qualMatrixList, isR2=FALSE, xScale=1, ySca
       qm = qualMatrixList[[sampleName]]
       diffResult = signif(prop.table(qm,2)*100, digits=3) - avgQual[1:nrow(qm), 1:ncol(qm)]
       pngFileName = plotQualityHeatmap(diffResult, colorRange=c(minDiff, maxDiff), 
-                                       pngFileName=paste("diffReadsQuality-heatmap_", sampleName, ".png", sep=""),
+                                       pngFileName=paste0("diffReadsQuality-heatmap_", sampleName, ".png"),
                                        colors=ezRedBlueScale(256), main=paste("diffReadsQuality", sampleName, sep="_"),
                                        xScale=xScale, yScale=yScale)
       pngTable[sampleName, nm] = pngFileName

R/app-fastqscreen.R

@@ -45,7 +45,7 @@ EzAppFastqScreen <-
 
 ## NOTEP: all 5 functions below get only called once each in ezMethodFastqScreen()
 executeFastqscreenCMD = function(param, files){
-  confFile = paste(FASTQSCREEN_CONF_DIR, param$confFile, sep="")
+  confFile = paste0(FASTQSCREEN_CONF_DIR, param$confFile)
   opt = ""
   if (param$nReads > 0){
     opt = paste(opt, "--subset", ezIntString(param$nReads))
@@ -63,7 +63,7 @@ executeFastqscreenCMD = function(param, files){
 executeBowtie2CMD = function(param, files){
   countFiles = character()
   for (nm in names(files)){
-    countFiles[nm] = paste(nm, "-counts.txt", sep="")
+    countFiles[nm] = paste0(nm, "-counts.txt")
     bowtie2options = param$cmdOptions
     if(!param$paired){
       cmd = paste(file.path(BOWTIE2_DIR,'bowtie2'),"-x",REFSEQ_mRNA_REF,