Mercurial > repos > lecorguille > camera_annotate

annotate lib.r @ 22:65e3e1a39e16 draft

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planemo upload commit 23ad0382ec59d66220fd94684a6d158fdef2c7f5-dirty
author lecorguille
date Fri, 22 Jul 2016 11:25:17 -0400
parents 339d92b2c503
children 2a4a811c663d
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1 # lib.r version="2.2.1"
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2
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3 #The function create a pdf from the different png generated by diffreport
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4 diffreport_png2pdf <- function(filebase, new_file_path) {
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6 pdfEicOutput = paste(new_file_path,filebase,"-eic_visible_pdf",sep="")
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7 pdfBoxOutput = paste(new_file_path,filebase,"-box_visible_pdf",sep="")
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9 system(paste("gm convert ",filebase,"_eic/*.png ",filebase,"_eic.pdf",sep=""))
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10 system(paste("gm convert ",filebase,"_box/*.png ",filebase,"_box.pdf",sep=""))
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12 file.copy(paste(filebase,"_eic.pdf",sep=""), pdfEicOutput)
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13 file.copy(paste(filebase,"_box.pdf",sep=""), pdfBoxOutput)
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14 }
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16 #The function annotateDiffreport without the corr function which bugs
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17 annotatediff <- function(xset=xset, listArguments=listArguments, variableMetadataOutput="variableMetadata.tsv", dataMatrixOutput="dataMatrix.tsv",new_file_path=NULL) {
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18 # Resolve the bug with x11, with the function png
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19 options(bitmapType='cairo')
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21 #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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22 res=try(is.null(xset@filled))
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23
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24 # ------ annot -------
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25 listArguments[["calcCiS"]]=as.logical(listArguments[["calcCiS"]])
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26 listArguments[["calcIso"]]=as.logical(listArguments[["calcIso"]])
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27 listArguments[["calcCaS"]]=as.logical(listArguments[["calcCaS"]])
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29 # common parameters
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30 listArguments4annotate = list(object=xset,
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31 nSlaves=listArguments[["nSlaves"]],sigma=listArguments[["sigma"]],perfwhm=listArguments[["perfwhm"]],
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32 maxcharge=listArguments[["maxcharge"]],maxiso=listArguments[["maxiso"]],minfrac=listArguments[["minfrac"]],
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33 ppm=listArguments[["ppm"]],mzabs=listArguments[["mzabs"]],quick=listArguments[["quick"]],
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34 polarity=listArguments[["polarity"]],max_peaks=listArguments[["max_peaks"]],intval=listArguments[["intval"]])
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35
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36 # quick == FALSE
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37 if(listArguments[["quick"]]==FALSE) {
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38 listArguments4annotate = append(listArguments4annotate,
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39 list(graphMethod=listArguments[["graphMethod"]],cor_eic_th=listArguments[["cor_eic_th"]],pval=listArguments[["pval"]],
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40 calcCiS=listArguments[["calcCiS"]],calcIso=listArguments[["calcIso"]],calcCaS=listArguments[["calcCaS"]]))
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41 # no ruleset
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42 if (!is.null(listArguments[["multiplier"]])) {
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43 listArguments4annotate = append(listArguments4annotate,
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44 list(multiplier=listArguments[["multiplier"]]))
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45 }
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46 # ruleset
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47 else {
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48 rulset=read.table(listArguments[["rules"]], h=T, sep=";")
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49 if (ncol(rulset) < 4) rulset=read.table(listArguments[["rules"]], h=T, sep="\t")
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50 if (ncol(rulset) < 4) rulset=read.table(listArguments[["rules"]], h=T, sep=",")
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51 if (ncol(rulset) < 4) {
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52 error_message="Your ruleset file seems not well formatted. The column separators accepted are ; , and tabulation"
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53 print(error_message)
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54 stop(error_message)
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55 }
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56
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57 listArguments4annotate = append(listArguments4annotate,
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58 list(rules=rulset))
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59 }
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60 }
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61
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62 # launch annotate
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63 xa = do.call("annotate", listArguments4annotate)
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64 peakList=getPeaklist(xa,intval=listArguments[["intval"]])
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65 peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");
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66
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67
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68 # --- Multi condition : diffreport ---
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69 diffrep=NULL
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70 if (!is.null(listArguments[["runDiffreport"]]) & nlevels(sampclass(xset))>=2) {
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71 #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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72 res=try(is.null(xset@filled))
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73 classes=levels(sampclass(xset))
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74 x=1:(length(classes)-1)
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75 for (i in seq(along=x) ) {
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76 y=1:(length(classes))
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77 for (n in seq(along=y)){
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78 if(i+n <= length(classes)){
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79 filebase=paste(classes[i],class2=classes[i+n],sep="-vs-")
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80
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81 diffrep=diffreport(object=xset,class1=classes[i],class2=classes[i+n],filebase=filebase,eicmax=listArguments[["eicmax"]],eicwidth=listArguments[["eicwidth"]],sortpval=TRUE,value=listArguments[["value"]],h=listArguments[["h"]],w=listArguments[["w"]],mzdec=listArguments[["mzdec"]])
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82 #combines results
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83 diffreportTSV=merge(peakList, diffrep[,c("name","fold","tstat","pvalue")], by.x="name", by.y="name", sort=F)
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84 diffreportTSV=cbind(diffreportTSV[,!(colnames(diffreportTSV) %in% c(sampnames(xa@xcmsSet)))],diffreportTSV[,(colnames(diffreportTSV) %in% c(sampnames(xa@xcmsSet)))])
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85
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86 if(listArguments[["sortpval"]]){
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87 diffreportTSV=diffreportTSV[order(diffreportTSV$pvalue), ]
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88 }
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89
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90 if (listArguments[["convert_param"]]){
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91 #converting the retention times (seconds) into minutes
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92 diffreportTSV$rt=diffreportTSV$rt/60;diffreportTSV$rtmin=diffreportTSV$rtmin/60; diffreportTSV$rtmax=diffreportTSV$rtmax/60;
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93 }
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94 write.table(diffreportTSV, sep="\t", quote=FALSE, row.names=FALSE, file=paste(new_file_path,filebase,"-tabular_visible_tabular",sep=""))
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95
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96 if (listArguments[["eicmax"]] != 0) {
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97 diffreport_png2pdf(filebase, new_file_path)
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98 }
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99 }
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100 }
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101 }
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102 }
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103
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104
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105
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106
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107 # --- variableMetadata ---
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108 variableMetadata=peakList[,!(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))]
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109 # if we have 2 conditions, we keep stat of diffrep
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110 if (!is.null(listArguments[["runDiffreport"]]) & nlevels(sampclass(xset))==2) {
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111 variableMetadata = merge(variableMetadata, diffrep[,c("name","fold","tstat","pvalue")],by.x="name", by.y="name", sort=F)
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112 if(exists("listArguments[[\"sortpval\"]]")){
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113 variableMetadata=variableMetadata[order(variableMetadata$pvalue), ]
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114 }
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115 }
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116
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117 variableMetadataOri=variableMetadata
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118 if (listArguments[["convert_param"]]){
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119 #converting the retention times (seconds) into minutes
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120 print("converting the retention times into minutes in the variableMetadata")
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121 variableMetadata$rt=variableMetadata$rt/60;variableMetadata$rtmin=variableMetadata$rtmin/60; variableMetadata$rtmax=variableMetadata$rtmax/60;
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122 }
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123 #Transform metabolites name
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124 variableMetadata$name= paste("M",round(variableMetadata$mz,digits=listArguments[["num_digits"]]),"T",round(variableMetadata$rt),sep="")
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125 write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput)
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126
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127 # --- dataMatrix ---
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128 dataMatrix = peakList[,(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))]
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129 dataMatrix=cbind(peakList$name,dataMatrix); colnames(dataMatrix)[1] = c("name");
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130
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131 if (listArguments[["convert_param"]]){
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132 #converting the retention times (seconds) into minutes
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133 print("converting the retention times into minutes in the dataMatrix ids")
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134 peakList$rt=peakList$rt/60
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135 }
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136 dataMatrix$name= paste("M",round(peakList$mz,digits=listArguments[["num_digits"]]),"T",round(peakList$rt),sep="")
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137 write.table(dataMatrix, sep="\t", quote=FALSE, row.names=FALSE, file=dataMatrixOutput)
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138
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139 return(list("xa"=xa,"diffrep"=diffrep,"variableMetadata"=variableMetadataOri));
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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 combinexsAnnos_function <- function(xaP, xaN, listOFlistArgumentsP,listOFlistArgumentsN, diffrepP=NULL,diffrepN=NULL,convert_param=FALSE,pos=TRUE,tol=2,ruleset=NULL,keep_meta=TRUE, variableMetadataOutput="variableMetadata.tsv"){
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145
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146 #Load the two Rdata to extract the xset objects from positive and negative mode
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147 cat("\tObject xset from positive mode\n")
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148 print(xaP)
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149 cat("\n")
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150
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151 cat("\tObject xset from negative mode\n")
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152 print(xaN)
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153 cat("\n")
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154
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155 cat("\n")
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156 cat("\tCombining...\n")
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157 #Convert the string to numeric for creating matrix
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158 row=as.numeric(strsplit(ruleset,",")[[1]][1])
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159 column=as.numeric(strsplit(ruleset,",")[[1]][2])
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160 ruleset=cbind(row,column)
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161 #Test if the file comes from an older version tool
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162 if ((!is.null(xaP)) & (!is.null(xaN))) {
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163 #Launch the combinexsannos function from CAMERA
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164 cAnnot=combinexsAnnos(xaP, xaN,pos=pos,tol=tol,ruleset=ruleset)
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165 } else {
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166 stop("You must relauch the CAMERA.annotate step with the lastest version.")
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167 }
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168
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169
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170
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171 if(pos){
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172 xa=xaP
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173 listOFlistArgumentsP=listOFlistArguments
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174 mode="neg. Mode"
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175 } else {
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176 xa=xaN
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177 listOFlistArgumentsN=listOFlistArguments
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178 mode="pos. Mode"
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179 }
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180 intval = "into"; for (steps in names(listOFlistArguments)) { if (!is.null(listOFlistArguments[[steps]]$intval)) intval = listOFlistArguments[[steps]]$intval }
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181 peakList=getPeaklist(xa,intval=intval)
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182 peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");
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183 variableMetadata=cbind(peakList, cAnnot[, c("isotopes", "adduct", "pcgroup",mode)]);
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184 variableMetadata=variableMetadata[,!(colnames(variableMetadata) %in% c(sampnames(xa@xcmsSet)))]
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185
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186 #Test if there are more than two classes (conditions)
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187 if ( nlevels(sampclass(xaP@xcmsSet))==2 & (!is.null(diffrepN)) & (!is.null(diffrepP))) {
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188 diffrepP = diffrepP[,c("name","fold","tstat","pvalue")]; colnames(diffrepP) = paste("P.",colnames(diffrepP),sep="")
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189 diffrepN = diffrepN[,c("name","fold","tstat","pvalue")]; colnames(diffrepN) = paste("N.",colnames(diffrepN),sep="")
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190
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191 variableMetadata = merge(variableMetadata, diffrepP, by.x="name", by.y="P.name")
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192 variableMetadata = merge(variableMetadata, diffrepN, by.x="name", by.y="N.name")
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193 }
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194
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195 rownames(variableMetadata) = NULL
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196 #TODO: checker
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197 #colnames(variableMetadata)[1:2] = c("name","mz/rt");
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198
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199 #If the user want to convert the retention times (seconds) into minutes.
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200 if (listArguments[["convert_param"]]){
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201 #converting the retention times (seconds) into minutes
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202 cat("\tConverting the retention times into minutes\n")
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203 variableMetadata$rtmed=cAnnot$rt/60; variableMetadata$rtmin=cAnnot$rtmin/60; variableMetadata$rtmax=cAnnot$rtmax/60;
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204 }
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205
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206 #If the user want to keep only the metabolites which match a difference
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207 if(keep_meta){
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208 variableMetadata=variableMetadata[variableMetadata[,c(mode)]!="",]
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209 }
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210
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211 #Write the output into a tsv file
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212 write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput)
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213 return(variableMetadata);
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214
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215 }