Mercurial > repos > mmonsoor > camera_combinexsannos

annotate CAMERA.r @ 9:972152941964 draft

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planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
author lecorguille
date Fri, 10 Feb 2017 11:11:49 -0500
parents 9a1a72ee9418
children d67f7aa847bf
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1 #!/usr/bin/env Rscript
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2 # CAMERA.r version="2.2.1"
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6 # ----- PACKAGE -----
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7 cat("\tPACKAGE INFO\n")
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9 setRepositories(graphics=F, ind=31)
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11 #pkgs=c("xcms","batch")
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12 pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","snow","igraph","CAMERA","multtest","batch")
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13 for(p in pkgs) {
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14 suppressPackageStartupMessages(suppressWarnings(library(p, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
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15 cat(p,"\t",as.character(packageVersion(p)),"\n",sep="")
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16 }
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17 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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19 cat("\n\n");
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23 # ----- ARGUMENTS -----
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24 cat("\tARGUMENTS INFO\n")
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26 listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
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27 write.table(as.matrix(listArguments), col.names=F, quote=F, sep='\t')
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29 cat("\n\n");
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32 # ----- PROCESSING INFILE -----
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33 cat("\tINFILE PROCESSING INFO\n")
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35 #image is an .RData file necessary to use xset variable given by previous tools
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36 if (!is.null(listArguments[["image"]])){
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37 load(listArguments[["image"]]); listArguments[["image"]]=NULL
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38 }
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40 if (listArguments[["xfunction"]] %in% c("combinexsAnnos")) {
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41 load(listArguments[["image_pos"]])
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42 xaP=xa
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43 listOFlistArgumentsP=listOFlistArguments
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44 if (exists("xsAnnotate_object")) xaP=xsAnnotate_object
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46 diffrepP=NULL
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47 if (exists("diffrep")) diffrepP=diffrep
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48
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49 load(listArguments[["image_neg"]])
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50 xaN=xa
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51 listOFlistArgumentsN=listOFlistArguments
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52 if (exists("xsAnnotate_object")) xaN=xsAnnotate_object
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54 diffrepN=NULL
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55 if (exists("diffrep")) diffrepN=diffrep
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56 }
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59 cat("\n\n")
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62 # ----- ARGUMENTS PROCESSING -----
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63 cat("\tARGUMENTS PROCESSING INFO\n")
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64
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65 # Save arguments to generate a report
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66 if (!exists("listOFlistArguments")) listOFlistArguments=list()
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67 listOFlistArguments[[paste(format(Sys.time(), "%y%m%d-%H:%M:%S_"),listArguments[["xfunction"]],sep="")]] = listArguments
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70 #saving the commun parameters
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71 thefunction = listArguments[["xfunction"]]
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72 listArguments[["xfunction"]]=NULL #delete from the list of arguments
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73
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74 xsetRdataOutput = paste(thefunction,"RData",sep=".")
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75 if (!is.null(listArguments[["xsetRdataOutput"]])){
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76 xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL
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77 }
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78
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79 rplotspdf = "Rplots.pdf"
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80 if (!is.null(listArguments[["rplotspdf"]])){
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81 rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL
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82 }
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83
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84 dataMatrixOutput = "dataMatrix.tsv"
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85 if (!is.null(listArguments[["dataMatrixOutput"]])){
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86 dataMatrixOutput = listArguments[["dataMatrixOutput"]]; listArguments[["dataMatrixOutput"]]=NULL
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87 }
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89 variableMetadataOutput = "variableMetadata.tsv"
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90 if (!is.null(listArguments[["variableMetadataOutput"]])){
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91 variableMetadataOutput = listArguments[["variableMetadataOutput"]]; listArguments[["variableMetadataOutput"]]=NULL
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92 }
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93
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94 if (!is.null(listArguments[["new_file_path"]])){
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95 new_file_path = listArguments[["new_file_path"]]; listArguments[["new_file_path"]]=NULL
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96 }
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97
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98 #Import the different functions
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99 source_local("lib.r")
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100
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101 #necessary to unzip .zip file uploaded to Galaxy
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102 #thanks to .zip file it's possible to upload many file as the same time conserving the tree hierarchy of directories
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103
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104 if (!is.null(listArguments[["zipfile"]])){
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105 zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL
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106 }
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107
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108 if (!is.null(listArguments[["singlefile_galaxyPath"]])){
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109 singlefile_galaxyPaths = unlist(strsplit(listArguments[["singlefile_galaxyPath"]],",")); listArguments[["singlefile_galaxyPath"]]=NULL
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110 singlefile_sampleNames = unlist(strsplit(listArguments[["singlefile_sampleName"]],",")); listArguments[["singlefile_sampleName"]]=NULL
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111
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112 singlefile=NULL
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113 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
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114 singlefile_galaxyPath=singlefile_galaxyPaths[singlefile_galaxyPath_i]
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115 singlefile_sampleName=singlefile_sampleNames[singlefile_galaxyPath_i]
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116 singlefile[[singlefile_sampleName]] = singlefile_galaxyPath
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117 }
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118 }
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119
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120 # We unzip automatically the chromatograms from the zip files.
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121 if (thefunction %in% c("annotatediff")) {
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122 if(exists("singlefile") && (length("singlefile")>0)) {
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123 for (singlefile_sampleName in names(singlefile)) {
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124 singlefile_galaxyPath = singlefile[[singlefile_sampleName]]
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125 if(!file.exists(singlefile_galaxyPath)){
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126 error_message=paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
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127 print(error_message); stop(error_message)
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128 }
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129
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130 file.symlink(singlefile_galaxyPath,singlefile_sampleName)
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131 }
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132 directory = "."
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133
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134
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135 }
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136 if(exists("zipfile") && (zipfile!="")) {
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137 if(!file.exists(zipfile)){
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138 error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
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139 print(error_message)
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140 stop(error_message)
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141 }
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142
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143 #list all file in the zip file
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144 #zip_files=unzip(zipfile,list=T)[,"Name"]
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145
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146 #unzip
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147 suppressWarnings(unzip(zipfile, unzip="unzip"))
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148
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149 #get the directory name
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150 filesInZip=unzip(zipfile, list=T);
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151 directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
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152 directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
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153 directory = "."
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154 if (length(directories) == 1) directory = directories
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155
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156 cat("files_root_directory\t",directory,"\n")
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157
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158 }
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159 }
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160
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161
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162 #addition of xset object to the list of arguments in the first position
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163 if (exists("xset") != 0){
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164 listArguments=append(list(xset), listArguments)
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165 }
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166
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167 cat("\n\n")
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168
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169
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170
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171
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172 # ----- PROCESSING INFO -----
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173 cat("\tMAIN PROCESSING INFO\n")
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174
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175 #change the default display settings
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176 pdf(file=rplotspdf, width=16, height=12)
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177
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178
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179 if (thefunction %in% c("annotatediff")) {
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180 results_list=annotatediff(xset=xset,listArguments=listArguments,variableMetadataOutput=variableMetadataOutput,dataMatrixOutput=dataMatrixOutput,new_file_path=new_file_path)
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181 xa=results_list[["xa"]]
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182 diffrep=results_list[["diffrep"]]
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183 variableMetadata=results_list[["variableMetadata"]]
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184
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185 cat("\n\n")
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186 cat("\tXSET OBJECT INFO\n")
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187 print(xa)
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188 }
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189
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190 if (thefunction %in% c("combinexsAnnos")) {
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191 cAnnot=combinexsAnnos_function(
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192 xaP=xaP,xaN=xaN,
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193 listOFlistArgumentsP=listOFlistArgumentsP,listOFlistArgumentsN=listOFlistArgumentsN,
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194 diffrepP=diffrepP,diffrepN=diffrepN,
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195 pos=listArguments[["pos"]],tol=listArguments[["tol"]],ruleset=listArguments[["ruleset"]],keep_meta=listArguments[["keep_meta"]],
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196 intval=listArguments[["intval"]], convertRTMinute=listArguments[["convertRTMinute"]], numDigitsMZ=listArguments[["numDigitsMZ"]], numDigitsRT=listArguments[["numDigitsRT"]],
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197 variableMetadataOutput=variableMetadataOutput
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198 )
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199 }
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200
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201 dev.off()
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202
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203
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204 #saving R data in .Rdata file to save the variables used in the present tool
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205 objects2save = c("xa","variableMetadata","diffrep","cAnnot","listOFlistArguments","zipfile")
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206 save(list=objects2save[objects2save %in% ls()], file=xsetRdataOutput)
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207
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208 cat("\n\n")
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209
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210 cat("\tDONE\n")