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annotate xcms.r @ 29:c013ed353a2f draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
author lecorguille
date Tue, 13 Feb 2018 04:44:03 -0500
parents 30410a052ab3
children
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1 #!/usr/bin/env Rscript
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2 # xcms.r version="2.2.0"
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3 #Authors ABIMS TEAM
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4 #BPC Addition from Y.guitton
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7 # ----- LOG FILE -----
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8 log_file=file("log.txt", open = "wt")
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9 sink(log_file)
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10 sink(log_file, type = "output")
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13 # ----- PACKAGE -----
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14 cat("\tPACKAGE INFO\n")
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15 #pkgs=c("xcms","batch")
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16 pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","snow","batch")
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17 for(pkg in pkgs) {
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18 suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
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19 cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="")
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20 }
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21 source_local <- function(fname){ argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
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22 cat("\n\n");
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28 # ----- ARGUMENTS -----
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29 cat("\tARGUMENTS INFO\n")
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30 listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
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31 write.table(as.matrix(listArguments), col.names=F, quote=F, sep='\t')
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32
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33 cat("\n\n");
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36 # ----- ARGUMENTS PROCESSING -----
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37 cat("\tINFILE PROCESSING INFO\n")
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39 #image is an .RData file necessary to use xset variable given by previous tools
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40 if (!is.null(listArguments[["image"]])){
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41 load(listArguments[["image"]]); listArguments[["image"]]=NULL
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42 }
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44 #Import the different functions
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45 source_local("lib.r")
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47 cat("\n\n")
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49 #Import the different functions
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50
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51 # ----- PROCESSING INFILE -----
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52 cat("\tARGUMENTS PROCESSING INFO\n")
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54 # Save arguments to generate a report
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55 if (!exists("listOFlistArguments")) listOFlistArguments=list()
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56 listOFlistArguments[[paste(format(Sys.time(), "%y%m%d-%H:%M:%S_"),listArguments[["xfunction"]],sep="")]] = listArguments
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58
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59 #saving the commun parameters
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60 thefunction = listArguments[["xfunction"]]; listArguments[["xfunction"]]=NULL #delete from the list of arguments
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62 xsetRdataOutput = paste(thefunction,"RData",sep=".")
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63 if (!is.null(listArguments[["xsetRdataOutput"]])){
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64 xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL
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65 }
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66
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67 #saving the specific parameters
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68 rplotspdf = "Rplots.pdf"
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69 if (!is.null(listArguments[["rplotspdf"]])){
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70 rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL
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71 }
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72 sampleMetadataOutput = "sampleMetadata.tsv"
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73 if (!is.null(listArguments[["sampleMetadataOutput"]])){
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74 sampleMetadataOutput = listArguments[["sampleMetadataOutput"]]; listArguments[["sampleMetadataOutput"]]=NULL
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75 }
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76 variableMetadataOutput = "variableMetadata.tsv"
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77 if (!is.null(listArguments[["variableMetadataOutput"]])){
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78 variableMetadataOutput = listArguments[["variableMetadataOutput"]]; listArguments[["variableMetadataOutput"]]=NULL
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79 }
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80 dataMatrixOutput = "dataMatrix.tsv"
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81 if (!is.null(listArguments[["dataMatrixOutput"]])){
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82 dataMatrixOutput = listArguments[["dataMatrixOutput"]]; listArguments[["dataMatrixOutput"]]=NULL
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83 }
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84 if (!is.null(listArguments[["convertRTMinute"]])){
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85 convertRTMinute = listArguments[["convertRTMinute"]]; listArguments[["convertRTMinute"]]=NULL
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86 }
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87 if (!is.null(listArguments[["numDigitsMZ"]])){
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88 numDigitsMZ = listArguments[["numDigitsMZ"]]; listArguments[["numDigitsMZ"]]=NULL
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89 }
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90 if (!is.null(listArguments[["numDigitsRT"]])){
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91 numDigitsRT = listArguments[["numDigitsRT"]]; listArguments[["numDigitsRT"]]=NULL
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92 }
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93 if (!is.null(listArguments[["intval"]])){
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94 intval = listArguments[["intval"]]; listArguments[["intval"]]=NULL
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95 }
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97 if (thefunction %in% c("xcmsSet","retcor")) {
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98 ticspdf = listArguments[["ticspdf"]]; listArguments[["ticspdf"]]=NULL
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99 bicspdf = listArguments[["bicspdf"]]; listArguments[["bicspdf"]]=NULL
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100 }
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101
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103 if (thefunction %in% c("xcmsSet","retcor","fillPeaks")) {
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104 if (!exists("singlefile")) singlefile=NULL
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105 if (!exists("zipfile")) zipfile=NULL
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106 rawFilePath = getRawfilePathFromArguments(singlefile, zipfile, listArguments)
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107 zipfile = rawFilePath$zipfile
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108 singlefile = rawFilePath$singlefile
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109 listArguments = rawFilePath$listArguments
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110 directory = retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
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111 md5sumList=list("origin"=getMd5sum(directory))
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112 }
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113
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114 #addition of the directory to the list of arguments in the first position
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115 if (thefunction == "xcmsSet") {
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116 checkXmlStructure(directory)
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117 checkFilesCompatibilityWithXcms(directory)
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118 listArguments=append(directory, listArguments)
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119 }
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120
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121
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122 #addition of xset object to the list of arguments in the first position
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123 if (exists("xset")){
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124 listArguments=append(list(xset), listArguments)
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125 }
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126
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127 cat("\n\n")
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128
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129
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130
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131
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132 # ----- MAIN PROCESSING INFO -----
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133 cat("\tMAIN PROCESSING INFO\n")
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134
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135
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136 #Verification of a group step before doing the fillpeaks job.
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137
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138 if (thefunction == "fillPeaks") {
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139 res=try(is.null(groupnames(xset)))
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140 if (class(res) == "try-error"){
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141 error<-geterrmessage()
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142 write(error, stderr())
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143 stop("You must always do a group step after a retcor. Otherwise it won't work for the fillpeaks step")
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144 }
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145
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146 }
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147
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148 #change the default display settings
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149 #dev.new(file="Rplots.pdf", width=16, height=12)
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150 pdf(file=rplotspdf, width=16, height=12)
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151 if (thefunction == "group") {
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152 par(mfrow=c(2,2))
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153 }
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154 #else if (thefunction == "retcor") {
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155 #try to change the legend display
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156 # par(xpd=NA)
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157 # par(xpd=T, mar=par()$mar+c(0,0,0,4))
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158 #}
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159
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160
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161 #execution of the function "thefunction" with the parameters given in "listArguments"
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162
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163 cat("\t\tCOMPUTE\n")
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164 xset = do.call(thefunction, listArguments)
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165
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166 # check if there are no peaks
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167 if (nrow(peaks(xset)) == 0) {
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168 stop("No peaks were detected. You should review your settings")
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169 }
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170
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171
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172 cat("\n\n")
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173
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174 dev.off() #dev.new(file="Rplots.pdf", width=16, height=12)
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175
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176 if (thefunction == "xcmsSet") {
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177
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178 #transform the files absolute pathways into relative pathways
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179 xset@filepaths<-sub(paste(getwd(),"/",sep="") ,"", xset@filepaths)
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180 if(exists("zipfile") && !is.null(zipfile) && (zipfile!="")) {
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181
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182 #Modify the samples names (erase the path)
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183 for(i in 1:length(sampnames(xset))){
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184
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185 sample_name=unlist(strsplit(sampnames(xset)[i], "/"))
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186 sample_name=sample_name[length(sample_name)]
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187 sample_name= unlist(strsplit(sample_name,"[.]"))[1]
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188 sampnames(xset)[i]=sample_name
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189
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190 }
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191
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192 }
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193
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194 }
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195
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196 # -- TIC --
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197 if (thefunction == "xcmsSet") {
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198 cat("\t\tGET TIC GRAPH\n")
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199 sampleNamesList = getSampleMetadata(xcmsSet=xset, sampleMetadataOutput=sampleMetadataOutput)
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200 getTICs(xcmsSet=xset, pdfname=ticspdf,rt="raw")
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201 getBPCs(xcmsSet=xset,rt="raw",pdfname=bicspdf)
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202 } else if (thefunction == "retcor") {
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203 cat("\t\tGET TIC GRAPH\n")
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204 getTICs(xcmsSet=xset, pdfname=ticspdf,rt="corrected")
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205 getBPCs(xcmsSet=xset,rt="corrected",pdfname=bicspdf)
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206 }
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207
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208 if ((thefunction == "group" || thefunction == "fillPeaks") && exists("intval")) {
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209 getPeaklistW4M(xset,intval,convertRTMinute,numDigitsMZ,numDigitsRT,variableMetadataOutput,dataMatrixOutput)
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210 }
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211
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212
6
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213 cat("\n\n")
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214
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215 # ----- EXPORT -----
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216
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217 cat("\tXSET OBJECT INFO\n")
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218 print(xset)
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219 #delete the parameters to avoid the passage to the next tool in .RData image
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220
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221
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222 #saving R data in .Rdata file to save the variables used in the present tool
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223 objects2save = c("xset","zipfile","singlefile","listOFlistArguments","md5sumList","sampleNamesList")
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224 save(list=objects2save[objects2save %in% ls()], file=xsetRdataOutput)
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226 cat("\n\n")
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229 cat("\tDONE\n")