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1 args<-commandArgs(TRUE)
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2
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3 chrom=args[1]
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4 dataset=args[2]
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5 output=args[3]
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6 tmp_dir=args[4]
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7 input=args[5]
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8 tumorcsv=args[6]
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9 signal=args[7]
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10 snp=type.convert(args[8])
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11 user=args[9]
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12 symmetrize=args[10]
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13
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14 library(MPAgenomics)
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15 workdir=file.path(tmp_dir, "mpagenomics",user)
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16 setwd(workdir)
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17
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18
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19 if (grepl("all",tolower(chrom)) | chrom=="None") {
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20 chrom_vec=c(1:25)
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21 } else {
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22 chrom_tmp <- strsplit(chrom,",")
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23 chrom_vecstring <-unlist(chrom_tmp)
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24 chrom_vec <- as.numeric(chrom_vecstring)
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25 }
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26 if (signal == "CN")
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27 {
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28 if (input == "dataset") {
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29 if (tumorcsv== "None")
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30 {
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31 CN=getCopyNumberSignal(dataset,chromosome=chrom_vec, onlySNP=snp)
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32
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33 } else {
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34 CN=getCopyNumberSignal(dataset,chromosome=chrom_vec, normalTumorArray=tumorcsv, onlySNP=snp)
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35 }
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36 } else {
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37 input_tmp <- strsplit(input,",")
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38 input_tmp_vecstring <-unlist(input_tmp)
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39 input_vecstring = sub("^([^.]*).*", "\\1", input_tmp_vecstring)
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40 if (tumorcsv== "None")
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41 {
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42 CN=getCopyNumberSignal(dataset,chromosome=chrom_vec, listOfFiles=input_vecstring, onlySNP=snp)
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43 } else {
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44 CN=getCopyNumberSignal(dataset,chromosome=chrom_vec, normalTumorArray=tumorcsv, listOfFiles=input_vecstring, onlySNP=snp )
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45 }
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46 }
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47
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48 list_chr=names(CN)
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49 CN_global=data.frame(check.names = FALSE)
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50 for (i in list_chr) {
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51 chr_data=data.frame(CN[[i]],check.names = FALSE)
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52 CN_global=rbind(CN_global,chr_data)
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53 }
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54 names(CN_global)[names(CN_global)=="featureNames"] <- "probeName"
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55 write.table(format(CN_global), output, row.names = FALSE, quote = FALSE, sep = "\t")
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56
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57 } else {
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58 if (symmetrize=="TRUE") {
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59 if (input == "dataset") {
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60 input_vecstring = getListOfFiles(dataset)
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61 } else {
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62 input_tmp <- strsplit(input,",")
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63 input_tmp_vecstring <-unlist(input_tmp)
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64 input_vecstring = sub("^([^.]*).*", "\\1", input_tmp_vecstring)
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65 }
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66
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67 symFracB_global=data.frame(check.names = FALSE)
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68
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69 for (currentFile in input_vecstring) {
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70 cat(paste0("extracting signal from ",currentFile,".\n"))
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71 currentSymFracB=data.frame()
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72 symFracB=getSymFracBSignal(dataset,chromosome=chrom_vec,file=currentFile,normalTumorArray=tumorcsv)
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73 list_chr=names(symFracB)
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74 for (i in list_chr) {
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75 cat(paste0(" extracting ",i,".\n"))
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76 chr_data=data.frame(symFracB[[i]]$tumor,check.names = FALSE)
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77 currentSymFracB=rbind(currentSymFracB,chr_data)
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78
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79 }
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80 if (is.null(symFracB_global) || nrow(symFracB_global)==0) {
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81 symFracB_global=currentSymFracB
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82 } else {
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83 symFracB_global=cbind(symFracB_global,currentFile=currentSymFracB[[3]])
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84 }
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85 }
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86 names(symFracB_global)[names(symFracB_global)=="featureNames"] <- "probeName"
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87
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88 write.table(format(symFracB_global), output, row.names = FALSE, quote = FALSE, sep = "\t")
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89 } else {
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90 if (input == "dataset") {
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91 if (tumorcsv== "None")
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92 {
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93 fracB=getFracBSignal(dataset,chromosome=chrom_vec)
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94
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95 } else {
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96 fracB=getFracBSignal(dataset,chromosome=chrom_vec, normalTumorArray=tumorcsv)
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97 }
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98 } else {
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99 input_tmp <- strsplit(input,",")
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100 input_tmp_vecstring <-unlist(input_tmp)
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101 input_vecstring = sub("^([^.]*).*", "\\1", input_tmp_vecstring)
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102 if (tumorcsv== "None")
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103 {
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104 fracB=getFracBSignal(dataset,chromosome=chrom_vec, listOfFiles=input_vecstring)
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105 } else {
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106 fracB=getFracBSignal(dataset,chromosome=chrom_vec, normalTumorArray=tumorcsv, listOfFiles=input_vecstring)
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107 }
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108 }
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109 #formatage des données
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110 list_chr=names(fracB)
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111 fracB_global=data.frame(check.names = FALSE)
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112 for (i in list_chr) {
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113 chr_data=data.frame(fracB[[i]]$tumor,check.names = FALSE)
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114 fracB_global=rbind(fracB_global,chr_data)
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115 }
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116 names(fracB_global)[names(fracB_global)=="featureNames"] <- "probeName"
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117 write.table(format(fracB_global), output, row.names = FALSE, quote = FALSE, sep = "\t")
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118 }
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119
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120 } |
