Mercurial > repos > lecorguille > xcms_xcmsset

annotate lib.r @ 8:53923784176c draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
author lecorguille
date Mon, 04 Jul 2016 08:45:48 -0400
parents 0888f7ef739a
children 91311aa08cdc
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0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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1 # lib.r version="2.0.1"
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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2 #Authors ABiMS TEAM
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3 #Lib.r for Galaxy Workflow4Metabo
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4 #version 2.2
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5 #Based on lib.r 2.1
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6 #Modifications made by Guitton Yann
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7 #correct bug in Base Peak Chromatogram (BPC) option, not only TIC when scanrange used in xcmsSet
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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8 #Note if scanrange is used a warning is prompted in R console but do not stop PDF generation
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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13 #@author Y. Guitton
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14 getBPC <- function(file,rtcor=NULL, ...) {
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15 object <- xcmsRaw(file)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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16 sel <- profRange(object, ...)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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17 cbind(if (is.null(rtcor)) object@scantime[sel$scanidx] else rtcor ,xcms:::colMax(object@env$profile[sel$massidx,sel$scanidx,drop=FALSE]))
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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18 #plotChrom(xcmsRaw(file), base=T)
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19 }
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21 #@author Y. Guitton
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22 getBPCs <- function (xcmsSet=NULL, pdfname="BPCs.pdf",rt=c("raw","corrected"), scanrange=NULL) {
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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23 cat("Creating BIC pdf...\n")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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25 if (is.null(xcmsSet)) {
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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26 cat("Enter an xcmsSet \n")
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27 stop()
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28 } else {
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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29 files <- filepaths(xcmsSet)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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30 }
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32 class<-as.vector(levels(xcmsSet@phenoData[,1])) #sometime phenoData have more than 1 column use first as class
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34 classnames<-vector("list",length(class))
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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35 for (i in 1:length(class)){
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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36 classnames[[i]]<-which( xcmsSet@phenoData[,1]==class[i])
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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37 }
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39 N <- dim(phenoData(xcmsSet))[1]
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41 TIC <- vector("list",N)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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44 for (j in 1:N) {
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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46 TIC[[j]] <- getBPC(files[j])
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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47 #good for raw
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48 # seems strange for corrected
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49 #errors if scanrange used in xcmsSetgeneration
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50 if (!is.null(xcmsSet) && rt == "corrected")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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51 rtcor <- xcmsSet@rt$corrected[[j]] else
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52 rtcor <- NULL
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54 TIC[[j]] <- getBPC(files[j],rtcor=rtcor)
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55 # TIC[[j]][,1]<-rtcor
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56 }
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60 pdf(pdfname,w=16,h=10)
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61 cols <- rainbow(N)
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62 lty = 1:N
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63 pch = 1:N
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64 #search for max x and max y in BPCs
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65 xlim = range(sapply(TIC, function(x) range(x[,1])))
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66 ylim = range(sapply(TIC, function(x) range(x[,2])))
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67 ylim = c(-ylim[2], ylim[2])
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70 ##plot start
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72 if (length(class)>2){
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73 for (k in 1:(length(class)-1)){
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74 for (l in (k+1):length(class)){
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75 #print(paste(class[k],"vs",class[l],sep=" "))
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76 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",class[k]," vs ",class[l], sep=""), xlab = "Retention Time (min)", ylab = "BPC")
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77 colvect<-NULL
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78 for (j in 1:length(classnames[[k]])) {
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79 tic <- TIC[[classnames[[k]][j]]]
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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80 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
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81 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
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82 colvect<-append(colvect,cols[classnames[[k]][j]])
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83 }
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84 for (j in 1:length(classnames[[l]])) {
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85 # i=class2names[j]
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86 tic <- TIC[[classnames[[l]][j]]]
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87 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
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88 colvect<-append(colvect,cols[classnames[[l]][j]])
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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89 }
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90 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
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91 }
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92 }
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93 }#end if length >2
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95 if (length(class)==2){
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96 k=1
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97 l=2
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98 colvect<-NULL
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99 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",class[k],"vs",class[l], sep=""), xlab = "Retention Time (min)", ylab = "BPC")
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100
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101 for (j in 1:length(classnames[[k]])) {
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102
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103 tic <- TIC[[classnames[[k]][j]]]
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104 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
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105 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
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lecorguille
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106 colvect<-append(colvect,cols[classnames[[k]][j]])
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107 }
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108 for (j in 1:length(classnames[[l]])) {
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parents:
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109 # i=class2names[j]
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lecorguille
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110 tic <- TIC[[classnames[[l]][j]]]
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lecorguille
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111 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
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lecorguille
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112 colvect<-append(colvect,cols[classnames[[l]][j]])
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113 }
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lecorguille
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114 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
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115
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116 }#end length ==2
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117
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118 dev.off() #pdf(pdfname,w=16,h=10)
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119
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120 invisible(TIC)
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121 }
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122
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123
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124
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lecorguille
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125 #@author Y. Guitton
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126 getTIC <- function(file,rtcor=NULL) {
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lecorguille
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127 object <- xcmsRaw(file)
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128 cbind(if (is.null(rtcor)) object@scantime else rtcor, rawEIC(object,mzrange=range(object@env$mz))$intensity)
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lecorguille
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129 }
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130
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lecorguille
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131 ##
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132 ## overlay TIC from all files in current folder or from xcmsSet, create pdf
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133 ##
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lecorguille
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diff changeset
134 #@author Y. Guitton
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135 getTICs <- function(xcmsSet=NULL,files=NULL, pdfname="TICs.pdf",rt=c("raw","corrected")) {
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lecorguille
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136 cat("Creating TIC pdf...\n")
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diff changeset
137
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138 if (is.null(xcmsSet)) {
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lecorguille
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139 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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140 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|")
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lecorguille
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141 if (is.null(files))
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142 files <- getwd()
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lecorguille
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143 info <- file.info(files)
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lecorguille
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144 listed <- list.files(files[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE)
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lecorguille
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145 files <- c(files[!info$isdir], listed)
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lecorguille
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146 } else {
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147 files <- filepaths(xcmsSet)
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148 }
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149
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150 class<-as.vector(levels(xcmsSet@phenoData[,1])) #sometime phenoData have more than 1 column use first as class
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151
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152 classnames<-vector("list",length(class))
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diff changeset
153 for (i in 1:length(class)){
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154 classnames[[i]]<-which( xcmsSet@phenoData[,1]==class[i])
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155 }
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156
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157 N <- length(files)
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158 TIC <- vector("list",N)
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159
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160 for (i in 1:N) {
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diff changeset
161 if (!is.null(xcmsSet) && rt == "corrected")
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162 rtcor <- xcmsSet@rt$corrected[[i]] else
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163 rtcor <- NULL
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164 TIC[[i]] <- getTIC(files[i],rtcor=rtcor)
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165 }
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166
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167 pdf(pdfname,w=16,h=10)
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parents:
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168 cols <- rainbow(N)
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169 lty = 1:N
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170 pch = 1:N
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171 #search for max x and max y in TICs
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172 xlim = range(sapply(TIC, function(x) range(x[,1])))
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173 ylim = range(sapply(TIC, function(x) range(x[,2])))
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174 ylim = c(-ylim[2], ylim[2])
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175
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176
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177 ##plot start
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178 if (length(class)>2){
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179 for (k in 1:(length(class)-1)){
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180 for (l in (k+1):length(class)){
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181 #print(paste(class[k],"vs",class[l],sep=" "))
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182 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Total Ion Chromatograms \n","TICs_",class[k]," vs ",class[l], sep=""), xlab = "Retention Time (min)", ylab = "TIC")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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183 colvect<-NULL
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184 for (j in 1:length(classnames[[k]])) {
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185
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186 tic <- TIC[[classnames[[k]][j]]]
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187 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
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188 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
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189 colvect<-append(colvect,cols[classnames[[k]][j]])
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190 }
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191 for (j in 1:length(classnames[[l]])) {
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192 # i=class2names[j]
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193 tic <- TIC[[classnames[[l]][j]]]
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194 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
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195 colvect<-append(colvect,cols[classnames[[l]][j]])
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196 }
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197 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
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198 }
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199 }
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200 }#end if length >2
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201 if (length(class)==2){
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202 k=1
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203 l=2
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204
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205 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Total Ion Chromatograms \n","TICs_",class[k],"vs",class[l], sep=""), xlab = "Retention Time (min)", ylab = "TIC")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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206 colvect<-NULL
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207 for (j in 1:length(classnames[[k]])) {
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208 tic <- TIC[[classnames[[k]][j]]]
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209 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
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lecorguille
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210 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
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lecorguille
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211 colvect<-append(colvect,cols[classnames[[k]][j]])
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212 }
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213 for (j in 1:length(classnames[[l]])) {
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214 # i=class2names[j]
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215 tic <- TIC[[classnames[[l]][j]]]
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216 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
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217 colvect<-append(colvect,cols[classnames[[l]][j]])
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218 }
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219 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
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220
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221 }#end length ==2
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lecorguille
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222 dev.off() #pdf(pdfname,w=16,h=10)
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223
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224 invisible(TIC)
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225 }
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226
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227
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228
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229 ##
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230 ## Get the polarities from all the samples of a condition
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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231 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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232 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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233 getSampleMetadata <- function(xcmsSet=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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234 cat("Creating the sampleMetadata file...\n")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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235
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236 #Create the sampleMetada dataframe
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237 sampleMetadata=xset@phenoData
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238 sampleNamesOrigin=rownames(sampleMetadata)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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239 sampleNamesMakeNames=make.names(sampleNamesOrigin)
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240
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241 if (any(duplicated(sampleNamesMakeNames))) {
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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242 write("\n\nERROR: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names().\nIn your case, at least two columns after the renaming obtain the same name, thus XCMS will collapse those columns per name.", stderr())
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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243 for (sampleName in sampleNamesOrigin) {
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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244 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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245 }
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246 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
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247 }
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248
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249 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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250 cat("\n\nWARNING: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names()\nIn your case, one or more sample names will be renamed in the sampleMetadata and dataMatrix files:\n")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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251 for (sampleName in sampleNamesOrigin) {
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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252 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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253 }
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254 }
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255
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256 sampleMetadata$sampleMetadata=sampleNamesMakeNames
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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257 sampleMetadata=cbind(sampleMetadata["sampleMetadata"],sampleMetadata["class"]) #Reorder columns
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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258 rownames(sampleMetadata)=NULL
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259
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260 #Create a list of files name in the current directory
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261 list_files=xset@filepaths
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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262 #For each sample file, the following actions are done
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
263 for (file in list_files){
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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264 #Check if the file is in the CDF format
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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265 if (!mzR:::netCDFIsFile(file)){
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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266
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267 # If the column isn't exist, with add one filled with NA
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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268 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity=NA
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269
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270 #Create a simple xcmsRaw object for each sample
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271 xcmsRaw=xcmsRaw(file)
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lecorguille
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272 #Extract the polarity (a list of polarities)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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273 polarity=xcmsRaw@polarity
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274 #Verify if all the scans have the same polarity
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275 uniq_list=unique(polarity)
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276 if (length(uniq_list)>1){
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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277 polarity="mixed"
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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278 } else {
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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279 polarity=as.character(uniq_list)
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280 }
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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281 #Transforms the character to obtain only the sample name
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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282 filename=basename(file)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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diff changeset
283 library(tools)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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284 samplename=file_path_sans_ext(filename)
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285
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286 #Set the polarity attribute
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287 sampleMetadata$polarity[sampleMetadata$sampleMetadata==samplename]=polarity
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288
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289 #Delete xcmsRaw object because it creates a bug for the fillpeaks step
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290 rm(xcmsRaw)
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291 }
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292
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293 }
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294
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295 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
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296
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297 return(list("sampleNamesOrigin"=sampleNamesOrigin,"sampleNamesMakeNames"=sampleNamesMakeNames))
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298
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299 }
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300
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301
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302 ##
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303 ## This function check if xcms will found all the files
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304 ##
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305 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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306 checkFilesCompatibilityWithXcms <- function(directory) {
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307 cat("Checking files filenames compatibilities with xmcs...\n")
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308 # WHAT XCMS WILL FIND
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309 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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310 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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311 info <- file.info(directory)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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312 listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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313 files <- c(directory[!info$isdir], listed)
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314 files_abs <- file.path(getwd(), files)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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315 exists <- file.exists(files_abs)
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316 files[exists] <- files_abs[exists]
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317 files[exists] <- sub("//","/",files[exists])
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318
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319 # WHAT IS ON THE FILESYSTEM
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320 filesystem_filepaths=system(paste("find $PWD/",directory," -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\"", sep=""), intern=T)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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321 filesystem_filepaths=filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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322
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323 # COMPARISON
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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324 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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325 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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326 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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327 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
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328
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329 }
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330 }
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331
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332
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333
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334 ##
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335 ## This function check if XML contains special caracters. It also checks integrity and completness.
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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336 ##
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337 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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338 checkXmlStructure <- function (directory) {
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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339 cat("Checking XML structure...\n")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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340
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341 cmd=paste("IFS=$'\n'; for xml in $(find",directory,"-not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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342 capture=system(cmd,intern=TRUE)
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343
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344 if (length(capture)>0){
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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345 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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346 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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347 write(capture, stderr())
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348 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
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349 }
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350
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351 }
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352
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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353
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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354 ##
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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355 ## This function check if XML contain special characters
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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356 ##
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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357 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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358 deleteXmlBadCharacters<- function (directory) {
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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359 cat("Checking Non ASCII characters in the XML...\n")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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diff changeset
360
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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diff changeset
361 processed=F
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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362 l=system( paste("find",directory, "-not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"),intern=TRUE)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
363 for (i in l){
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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364 cmd=paste("LC_ALL=C grep '[^ -~]' \"",i,"\"",sep="")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
365 capture=suppressWarnings(system(cmd,intern=TRUE))
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
366 if (length(capture)>0){
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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367 cmd=paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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368 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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369 c=system(cmd,intern=TRUE)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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370 capture=""
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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diff changeset
371 processed=T
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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372 }
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373 }
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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374 if (processed) cat("\n\n")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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375 return(processed)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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376 }
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377
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378
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379 ##
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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380 ## This function will compute MD5 checksum to check the data integrity
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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381 ##
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382 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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383 getMd5sum <- function (directory) {
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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384 cat("Compute md5 checksum...\n")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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385 # WHAT XCMS WILL FIND
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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386 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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387 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|")
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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388 info <- file.info(directory)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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389 listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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390 files <- c(directory[!info$isdir], listed)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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391 exists <- file.exists(files)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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392 files <- files[exists]
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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393
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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394 library(tools)
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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395
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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396 #cat("\n\n")
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397
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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398 return(as.matrix(md5sum(files)))
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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399 }
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400