Mercurial > repos > lecorguille > camera_annotate

annotate lib.r @ 20:b979ba5888f7 draft

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"planemo upload commit 0b77855ab98a4940d58727271c28990969367f4d"
author workflow4metabolomics
date Wed, 18 Mar 2020 06:36:02 -0400
parents 01459b73daf9
children abf1775ac14d
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1 # lib.r
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2
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3 #@author G. Le Corguille
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4 # solve an issue with batch if arguments are logical TRUE/FALSE
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5 parseCommandArgs <- function(...) {
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6 args <- batch::parseCommandArgs(...)
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7 for (key in names(args)) {
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8 if (args[key] %in% c("TRUE","FALSE"))
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9 args[key] = as.logical(args[key])
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10 }
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11 return(args)
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12 }
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14 #@author G. Le Corguille
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15 # This function will
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16 # - load the packages
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17 # - display the sessionInfo
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18 loadAndDisplayPackages <- function(pkgs) {
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19 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
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20
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21 sessioninfo = sessionInfo()
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22 cat(sessioninfo$R.version$version.string,"\n")
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23 cat("Main packages:\n")
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24 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
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25 cat("Other loaded packages:\n")
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26 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
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27 }
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29 # This function retrieve a xset like object
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30 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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31 getxcmsSetObject <- function(xobject) {
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32 # XCMS 1.x
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33 if (class(xobject) == "xcmsSet")
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34 return (xobject)
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35 # XCMS 3.x
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36 if (class(xobject) == "XCMSnExp") {
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37 # Get the legacy xcmsSet object
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38 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
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39 if (is.null(xset@phenoData$sample_group))
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40 sampclass(xset) = "."
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41 else
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42 sampclass(xset) <- xset@phenoData$sample_group
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43 if (!is.null(xset@phenoData$sample_name))
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44 rownames(xset@phenoData) = xset@phenoData$sample_name
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45 return (xset)
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46 }
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47 }
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48
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49 #@author G. Le Corguille
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50 #The function create a pdf from the different png generated by diffreport
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51 diffreport_png2pdf <- function(filebase) {
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52 dir.create("pdf")
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54 pdfEicOutput = paste0("pdf/",filebase,"-eic_pdf.pdf")
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55 pdfBoxOutput = paste0("pdf/",filebase,"-box_pdf.pdf")
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56
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57 system(paste0("gm convert ",filebase,"_eic/*.png ",pdfEicOutput))
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58 system(paste0("gm convert ",filebase,"_box/*.png ",pdfBoxOutput))
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59
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60 }
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62 #@author G. Le Corguille
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63 #The function create a zip archive from the different png generated by diffreport
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64 diffreport_png2zip <- function() {
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65 zip("eic.zip", dir(pattern="_eic"), zip=Sys.which("zip"))
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66 zip("box.zip", dir(pattern="_box"), zip=Sys.which("zip"))
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67 }
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68
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69 #The function create a zip archive from the different tabular generated by diffreport
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70 diffreport_tabular2zip <- function() {
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71 zip("tabular.zip", dir(pattern="tabular/*"), zip=Sys.which("zip"))
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72 }
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73
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74 #@author G. Le Corguille
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75 #This function convert if it is required the Retention Time in minutes
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76 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
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77 if (convertRTMinute){
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78 #converting the retention times (seconds) into minutes
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79 print("converting the retention times into minutes in the variableMetadata")
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80 variableMetadata[,"rt"]=variableMetadata[,"rt"]/60
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81 variableMetadata[,"rtmin"]=variableMetadata[,"rtmin"]/60
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82 variableMetadata[,"rtmax"]=variableMetadata[,"rtmax"]/60
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83 }
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84 return (variableMetadata)
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85 }
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86
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87 #@author G. Le Corguille
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88 #This function format ions identifiers
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89 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
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90 splitDeco = strsplit(as.character(variableMetadata$name),"_")
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91 idsDeco = sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
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92 namecustom = make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
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93 variableMetadata=cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
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94 return(variableMetadata)
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95 }
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97 #The function annotateDiffreport without the corr function which bugs
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98 annotatediff <- function(xset=xset, args=args, variableMetadataOutput="variableMetadata.tsv") {
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99 # Resolve the bug with x11, with the function png
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100 options(bitmapType='cairo')
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102 #Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped.
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103 res=try(is.null(xset@filled))
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104
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105 # ------ annot -------
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106 args$calcCiS=as.logical(args$calcCiS)
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107 args$calcIso=as.logical(args$calcIso)
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108 args$calcCaS=as.logical(args$calcCaS)
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109
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110 # common parameters
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111 args4annotate = list(object=xset,
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112 nSlaves=args$nSlaves,sigma=args$sigma,perfwhm=args$perfwhm,
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113 maxcharge=args$maxcharge,maxiso=args$maxiso,minfrac=args$minfrac,
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114 ppm=args$ppm,mzabs=args$mzabs,quick=args$quick,
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115 polarity=args$polarity,max_peaks=args$max_peaks,intval=args$intval)
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116
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117 # quick == FALSE
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118 if(args$quick==FALSE) {
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119 args4annotate = append(args4annotate,
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120 list(graphMethod=args$graphMethod,cor_eic_th=args$cor_eic_th,pval=args$pval,
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121 calcCiS=args$calcCiS,calcIso=args$calcIso,calcCaS=args$calcCaS))
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122 # no ruleset
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123 if (!is.null(args$multiplier)) {
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124 args4annotate = append(args4annotate,
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125 list(multiplier=args$multiplier))
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126 }
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127 # ruleset
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128 else {
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129 rulset=read.table(args$rules, h=T, sep=";")
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130 if (ncol(rulset) < 4) rulset=read.table(args$rules, h=T, sep="\t")
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131 if (ncol(rulset) < 4) rulset=read.table(args$rules, h=T, sep=",")
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132 if (ncol(rulset) < 4) {
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133 error_message="Your ruleset file seems not well formatted. The column separators accepted are ; , and tabulation"
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134 print(error_message)
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135 stop(error_message)
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136 }
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137
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138 args4annotate = append(args4annotate,
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139 list(rules=rulset))
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140 }
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141 }
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142
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143
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144 # launch annotate
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145 xa = do.call("annotate", args4annotate)
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146 peakList=getPeaklist(xa,intval=args$intval)
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147 peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");
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148
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149 # --- Multi condition : diffreport ---
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150 diffrepOri=NULL
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151 if (!is.null(args$runDiffreport) & nlevels(sampclass(xset))>=2) {
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152 #Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped.
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153 res=try(is.null(xset@filled))
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154 classes=levels(sampclass(xset))
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155 x=1:(length(classes)-1)
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156 for (i in seq(along=x) ) {
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157 y=1:(length(classes))
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158 for (n in seq(along=y)){
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159 if(i+n <= length(classes)){
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160 filebase=paste(classes[i],class2=classes[i+n],sep="-vs-")
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161
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162 diffrep=diffreport(
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163 object=xset,class1=classes[i],class2=classes[i+n],
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164 filebase=filebase,eicmax=args$eicmax,eicwidth=args$eicwidth,
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165 sortpval=TRUE,value=args$value,h=args$h,w=args$w,mzdec=args$mzdec,missing=0)
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166
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167 diffrepOri = diffrep
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168
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169 # renamming of the column rtmed to rt to fit with camera peaklist function output
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170 colnames(diffrep)[colnames(diffrep)=="rtmed"] <- "rt"
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171 colnames(diffrep)[colnames(diffrep)=="mzmed"] <- "mz"
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172
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173 # combines results and reorder columns
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174 diffrep = merge(peakList, diffrep[,c("name","fold","tstat","pvalue")], by.x="name", by.y="name", sort=F)
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175 diffrep = cbind(diffrep[,!(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))],diffrep[,(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))])
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176
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177 diffrep = RTSecondToMinute(diffrep, args$convertRTMinute)
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178 diffrep = formatIonIdentifiers(diffrep, numDigitsRT=args$numDigitsRT, numDigitsMZ=args$numDigitsMZ)
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179
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180 if(args$sortpval){
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181 diffrep=diffrep[order(diffrep$pvalue), ]
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182 }
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183
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184 dir.create("tabular", showWarnings = FALSE)
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185 write.table(diffrep, sep="\t", quote=FALSE, row.names=FALSE, file=paste("tabular/",filebase,"_tsv.tabular",sep=""))
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186
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187 if (args$eicmax != 0) {
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188 if (args$png2 == "pdf")
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189 diffreport_png2pdf(filebase)
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190 if (args$png2 == "zip")
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191 diffreport_png2zip()
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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 if (args$tabular2 == "zip")
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197 diffreport_tabular2zip()
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198 }
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199
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200 # --- variableMetadata ---
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201 variableMetadata=peakList[,!(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))]
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202 variableMetadata = RTSecondToMinute(variableMetadata, args$convertRTMinute)
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203 variableMetadata = formatIonIdentifiers(variableMetadata, numDigitsRT=args$numDigitsRT, numDigitsMZ=args$numDigitsMZ)
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204 # if we have 2 conditions, we keep stat of diffrep
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205 if (!is.null(args$runDiffreport) & nlevels(sampclass(xset))==2) {
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206 variableMetadata = merge(variableMetadata, diffrep[,c("name","fold","tstat","pvalue")],by.x="name", by.y="name", sort=F)
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207 if(exists("args[[\"sortpval\"]]")){
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208 variableMetadata=variableMetadata[order(variableMetadata$pvalue), ]
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209 }
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210 }
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211
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212 variableMetadataOri=variableMetadata
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213 write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput)
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214
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215 return(list("xa"=xa,"diffrep"=diffrepOri,"variableMetadata"=variableMetadataOri));
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216
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217 }
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218
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219
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220 combinexsAnnos_function <- function(xaP, xaN, diffrepP=NULL,diffrepN=NULL,
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221 pos=TRUE,tol=2,ruleset=NULL,keep_meta=TRUE, convertRTMinute=F, numDigitsMZ=0,
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222 numDigitsRT=0, variableMetadataOutput="variableMetadata.tsv"){
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223
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224 #Load the two Rdata to extract the xset objects from positive and negative mode
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225 cat("\tObject xset from positive mode\n")
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226 print(xaP)
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227 cat("\n")
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228
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229 cat("\tObject xset from negative mode\n")
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230 print(xaN)
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231 cat("\n")
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232
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233 cat("\n")
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234 cat("\tCombining...\n")
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235 #Convert the string to numeric for creating matrix
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236 row=as.numeric(strsplit(ruleset,",")[[1]][1])
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237 column=as.numeric(strsplit(ruleset,",")[[1]][2])
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238 ruleset=cbind(row,column)
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239 #Test if the file comes from an older version tool
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240 if ((!is.null(xaP)) & (!is.null(xaN))) {
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241 #Launch the combinexsannos function from CAMERA
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242 cAnnot=combinexsAnnos(xaP, xaN,pos=pos,tol=tol,ruleset=ruleset)
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243 } else {
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244 stop("You must relauch the CAMERA.annotate step with the lastest version.")
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245 }
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246
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247 if(pos){
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248 xa=xaP
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249 mode="neg. Mode"
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250 } else {
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251 xa=xaN
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252 mode="pos. Mode"
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253 }
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254
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255 peakList=getPeaklist(xa)
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256 peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");
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257 variableMetadata=cbind(peakList, cAnnot[, c("isotopes", "adduct", "pcgroup",mode)]);
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258 variableMetadata=variableMetadata[,!(colnames(variableMetadata) %in% c(sampnames(xa@xcmsSet)))]
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259
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260 #Test if there are more than two classes (conditions)
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261 if ( nlevels(sampclass(xaP@xcmsSet))==2 & (!is.null(diffrepN)) & (!is.null(diffrepP))) {
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262 diffrepP = diffrepP[,c("name","fold","tstat","pvalue")]; colnames(diffrepP) = paste("P.",colnames(diffrepP),sep="")
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263 diffrepN = diffrepN[,c("name","fold","tstat","pvalue")]; colnames(diffrepN) = paste("N.",colnames(diffrepN),sep="")
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264
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265 variableMetadata = merge(variableMetadata, diffrepP, by.x="name", by.y="P.name")
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266 variableMetadata = merge(variableMetadata, diffrepN, by.x="name", by.y="N.name")
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267 }
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268
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269 rownames(variableMetadata) = NULL
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270 #TODO: checker
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271 #colnames(variableMetadata)[1:2] = c("name","mz/rt");
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272
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273 variableMetadata = RTSecondToMinute(variableMetadata, convertRTMinute)
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274 variableMetadata = formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
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275
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276 #If the user want to keep only the metabolites which match a difference
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277 if(keep_meta){
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278 variableMetadata=variableMetadata[variableMetadata[,c(mode)]!="",]
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279 }
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280
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281 #Write the output into a tsv file
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282 write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput)
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283 return(variableMetadata);
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284
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285 }
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286
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287 # This function get the raw file path from the arguments
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288 getRawfilePathFromArguments <- function(singlefile, zipfile, args) {
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289 if (!is.null(args$zipfile)) zipfile = args$zipfile
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290 if (!is.null(args$zipfilePositive)) zipfile = args$zipfilePositive
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291 if (!is.null(args$zipfileNegative)) zipfile = args$zipfileNegative
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292
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293 if (!is.null(args$singlefile_galaxyPath)) {
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294 singlefile_galaxyPaths = args$singlefile_galaxyPath;
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295 singlefile_sampleNames = args$singlefile_sampleName
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296 }
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297 if (!is.null(args$singlefile_galaxyPathPositive)) {
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298 singlefile_galaxyPaths = args$singlefile_galaxyPathPositive;
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299 singlefile_sampleNames = args$singlefile_sampleNamePositive
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300 }
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301 if (!is.null(args$singlefile_galaxyPathNegative)) {
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302 singlefile_galaxyPaths = args$singlefile_galaxyPathNegative;
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303 singlefile_sampleNames = args$singlefile_sampleNameNegative
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304 }
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305 if (exists("singlefile_galaxyPaths")){
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306 singlefile_galaxyPaths = unlist(strsplit(singlefile_galaxyPaths,","))
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307 singlefile_sampleNames = unlist(strsplit(singlefile_sampleNames,","))
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308
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309 singlefile=NULL
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310 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
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311 singlefile_galaxyPath=singlefile_galaxyPaths[singlefile_galaxyPath_i]
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312 singlefile_sampleName=singlefile_sampleNames[singlefile_galaxyPath_i]
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313 singlefile[[singlefile_sampleName]] = singlefile_galaxyPath
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314 }
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315 }
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316 for (argument in c("zipfile", "zipfilePositive", "zipfileNegative",
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317 "singlefile_galaxyPath", "singlefile_sampleName",
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318 "singlefile_galaxyPathPositive", "singlefile_sampleNamePositive",
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319 "singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) {
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320 args[[argument]]=NULL
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321 }
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322 return(list(zipfile=zipfile, singlefile=singlefile, args=args))
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323 }
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324
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325
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326 # This function retrieve the raw file in the working directory
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327 # - if zipfile: unzip the file with its directory tree
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328 # - if singlefiles: set symlink with the good filename
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329 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
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330 if(!is.null(singlefile) && (length("singlefile")>0)) {
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331 for (singlefile_sampleName in names(singlefile)) {
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332 singlefile_galaxyPath = singlefile[[singlefile_sampleName]]
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333 if(!file.exists(singlefile_galaxyPath)){
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334 error_message=paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
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335 print(error_message); stop(error_message)
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336 }
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337
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338 file.symlink(singlefile_galaxyPath,singlefile_sampleName)
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339 }
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340 directory = "."
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341
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342 }
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343 if(!is.null(zipfile) && (zipfile!="")) {
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344 if(!file.exists(zipfile)){
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345 error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
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346 print(error_message)
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347 stop(error_message)
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348 }
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349
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350 #list all file in the zip file
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351 #zip_files=unzip(zipfile,list=T)[,"Name"]
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352
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353 #unzip
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354 suppressWarnings(unzip(zipfile, unzip="unzip"))
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355
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356 #get the directory name
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357 filesInZip=unzip(zipfile, list=T);
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358 directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
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359 directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
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360 directory = "."
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361 if (length(directories) == 1) directory = directories
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362
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363 cat("files_root_directory\t",directory,"\n")
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364
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365 }
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366 return (directory)
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367 }
16
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368