Mercurial > repos > lecorguille > xcms_plot_chromatogram

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
author workflow4metabolomics
date Mon, 11 Sep 2023 09:18:38 +0000
parents 024974037c4e
children
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c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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1 #@authors ABiMS TEAM, Y. Guitton
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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4 #@author G. Le Corguille
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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5 # solve an issue with batch if arguments are logical TRUE/FALSE
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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6 parseCommandArgs <- function(...) {
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8846a03995d3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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7 args <- batch::parseCommandArgs(...)
8846a03995d3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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8 for (key in names(args)) {
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9 if (args[key] %in% c("TRUE", "FALSE"))
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10 args[key] <- as.logical(args[key])
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11 }
8846a03995d3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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12 return(args)
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c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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13 }
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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15 #@author G. Le Corguille
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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16 # This function will
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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17 # - load the packages
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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18 # - display the sessionInfo
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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19 loadAndDisplayPackages <- function(pkgs) {
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20 for (pkg in pkgs) suppressPackageStartupMessages(stopifnot(library(pkg, quietly = TRUE, logical.return = TRUE, character.only = TRUE)))
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c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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21
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22 sessioninfo <- sessionInfo()
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23 cat(sessioninfo$R.version$version.string, "\n")
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24 cat("Main packages:\n")
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25 for (pkg in names(sessioninfo$otherPkgs)) {
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26 cat(paste(pkg, packageVersion(pkg)), "\t")
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27 }
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28 cat("\n")
8846a03995d3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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29 cat("Other loaded packages:\n")
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30 for (pkg in names(sessioninfo$loadedOnly)) {
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31 cat(paste(pkg, packageVersion(pkg)), "\t")
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32 }
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33 cat("\n")
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c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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34 }
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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36 #@author G. Le Corguille
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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37 # This function merge several chromBPI or chromTIC into one.
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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38 mergeChrom <- function(chrom_merged, chrom) {
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39 if (is.null(chrom_merged)) return(NULL)
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40 chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)
8846a03995d3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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41 return(chrom_merged)
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c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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42 }
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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44 #@author G. Le Corguille
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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45 # This function merge several xdata into one.
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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46 mergeXData <- function(args) {
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47 chromTIC <- NULL
8846a03995d3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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48 chromBPI <- NULL
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49 chromTIC_adjusted <- NULL
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50 chromBPI_adjusted <- NULL
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51 md5sumList <- NULL
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52 for (image in args$images) {
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53
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54 load(image)
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55 # Handle infiles
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56 if (!exists("singlefile")) singlefile <- NULL
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57 if (!exists("zipfile")) zipfile <- NULL
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58 rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
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59 zipfile <- rawFilePath$zipfile
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60 singlefile <- rawFilePath$singlefile
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61
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62 if (exists("raw_data")) xdata <- raw_data
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63 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
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64
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65 cat(sampleNamesList$sampleNamesOrigin, "\n")
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66
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67 if (!exists("xdata_merged")) {
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68 xdata_merged <- xdata
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69 singlefile_merged <- singlefile
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70 md5sumList_merged <- md5sumList
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71 sampleNamesList_merged <- sampleNamesList
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72 chromTIC_merged <- chromTIC
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73 chromBPI_merged <- chromBPI
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74 chromTIC_adjusted_merged <- chromTIC_adjusted
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75 chromBPI_adjusted_merged <- chromBPI_adjusted
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76 } else {
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77 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged, xdata)
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78 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged, xdata)
8846a03995d3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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79 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
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80
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81 singlefile_merged <- c(singlefile_merged, singlefile)
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82 md5sumList_merged$origin <- rbind(md5sumList_merged$origin, md5sumList$origin)
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83 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin, sampleNamesList$sampleNamesOrigin)
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84 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames, sampleNamesList$sampleNamesMakeNames)
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85 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC)
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86 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)
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87 chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)
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88 chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)
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89 }
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90 }
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91 rm(image)
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92 xdata <- xdata_merged
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93 rm(xdata_merged)
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94 singlefile <- singlefile_merged
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95 rm(singlefile_merged)
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96 md5sumList <- md5sumList_merged
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97 rm(md5sumList_merged)
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98 sampleNamesList <- sampleNamesList_merged
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99 rm(sampleNamesList_merged)
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100
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101 if (!is.null(args$sampleMetadata)) {
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102 cat("\tXSET PHENODATA SETTING...\n")
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103 sampleMetadataFile <- args$sampleMetadata
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104 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header = FALSE)
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105 xdata@phenoData@data$sample_group <- sampleMetadata$V2[match(xdata@phenoData@data$sample_name, sampleMetadata$V1)]
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106
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107 if (any(is.na(pData(xdata)$sample_group))) {
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108 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
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109 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse = " "))
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110 print(error_message)
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111 stop(error_message)
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112 }
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113 }
0
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114
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115 if (!is.null(chromTIC_merged)) {
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116 chromTIC <- chromTIC_merged
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117 chromTIC@phenoData <- xdata@phenoData
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118 }
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119 if (!is.null(chromBPI_merged)) {
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120 chromBPI <- chromBPI_merged
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121 chromBPI@phenoData <- xdata@phenoData
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122 }
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123 if (!is.null(chromTIC_adjusted_merged)) {
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124 chromTIC_adjusted <- chromTIC_adjusted_merged
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125 chromTIC_adjusted@phenoData <- xdata@phenoData
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126 }
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127 if (!is.null(chromBPI_adjusted_merged)) {
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128 chromBPI_adjusted <- chromBPI_adjusted_merged
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129 chromBPI_adjusted@phenoData <- xdata@phenoData
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130 }
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131
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132 return(list("xdata" = xdata, "singlefile" = singlefile, "md5sumList" = md5sumList, "sampleNamesList" = sampleNamesList, "chromTIC" = chromTIC, "chromBPI" = chromBPI, "chromTIC_adjusted" = chromTIC_adjusted, "chromBPI_adjusted" = chromBPI_adjusted))
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133 }
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134
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135 #@author G. Le Corguille
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136 # This function convert if it is required the Retention Time in minutes
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137 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
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138 if (convertRTMinute) {
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139 #converting the retention times (seconds) into minutes
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140 print("converting the retention times into minutes in the variableMetadata")
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141 variableMetadata[, "rt"] <- variableMetadata[, "rt"] / 60
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142 variableMetadata[, "rtmin"] <- variableMetadata[, "rtmin"] / 60
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143 variableMetadata[, "rtmax"] <- variableMetadata[, "rtmax"] / 60
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144 }
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145 return(variableMetadata)
0
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146 }
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147
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148 #@author G. Le Corguille
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149 # This function format ions identifiers
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150 formatIonIdentifiers <- function(variableMetadata, numDigitsRT = 0, numDigitsMZ = 0) {
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151 splitDeco <- strsplit(as.character(variableMetadata$name), "_")
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152 idsDeco <- sapply(splitDeco,
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153 function(x) {
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154 deco <- unlist(x)[2]
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155 if (is.na(deco)) return("") else return(paste0("_", deco))
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156 }
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157 )
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158 namecustom <- make.unique(paste0("M", round(variableMetadata[, "mz"], numDigitsMZ), "T", round(variableMetadata[, "rt"], numDigitsRT), idsDeco))
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159 variableMetadata <- cbind(name = variableMetadata$name, namecustom = namecustom, variableMetadata[, !(colnames(variableMetadata) %in% c("name"))])
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160 return(variableMetadata)
0
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161 }
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162
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163 #@author G. Le Corguille
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164 # This function convert the remain NA to 0 in the dataMatrix
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165 naTOzeroDataMatrix <- function(dataMatrix, naTOzero) {
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166 if (naTOzero) {
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167 dataMatrix[is.na(dataMatrix)] <- 0
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168 }
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169 return(dataMatrix)
0
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170 }
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171
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172 #@author G. Le Corguille
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173 # Draw the plotChromPeakDensity 3 per page in a pdf file
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174 getPlotChromPeakDensity <- function(xdata, param = NULL, mzdigit = 4) {
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175 pdf(file = "plotChromPeakDensity.pdf", width = 16, height = 12)
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176
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177 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
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178
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179 if (length(unique(xdata$sample_group)) < 10) {
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180 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
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181 } else {
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182 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
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183 }
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184 names(group_colors) <- unique(xdata$sample_group)
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185 col_per_samp <- as.character(xdata$sample_group)
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186 for (i in seq_len(length(group_colors))) {
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187 col_per_samp[col_per_samp == (names(group_colors)[i])] <- group_colors[i]
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188 }
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189
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190 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
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191 for (i in seq_len(nrow(featureDefinitions(xdata)))) {
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192 mzmin <- featureDefinitions(xdata)[i, ]$mzmin
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193 mzmax <- featureDefinitions(xdata)[i, ]$mzmax
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194 plotChromPeakDensity(xdata, param = param, mz = c(mzmin, mzmax), col = col_per_samp, pch = 16, xlim = xlim, main = paste(round(mzmin, mzdigit), round(mzmax, mzdigit)))
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195 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
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196 }
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197
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198 dev.off()
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199 }
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200
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201 #@author G. Le Corguille
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202 # Draw the plotChromPeakDensity 3 per page in a pdf file
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203 getPlotAdjustedRtime <- function(xdata) {
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204
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205 pdf(file = "raw_vs_adjusted_rt.pdf", width = 16, height = 12)
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206
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207 # Color by group
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208 if (length(unique(xdata$sample_group)) < 10) {
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209 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
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210 } else {
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211 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
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212 }
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213 if (length(group_colors) > 1) {
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214 names(group_colors) <- unique(xdata$sample_group)
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215 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
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216 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
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217 }
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218
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219 # Color by sample
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220 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
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221 legend("topright", legend = xdata@phenoData@data$sample_name, col = rainbow(length(xdata@phenoData@data$sample_name)), cex = 0.8, lty = 1)
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222
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223 dev.off()
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224 }
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225
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226 #@author G. Le Corguille
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227 # value: intensity values to be used into, maxo or intb
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228 getPeaklistW4M <- function(xdata, intval = "into", convertRTMinute = FALSE, numDigitsMZ = 4, numDigitsRT = 0, naTOzero = TRUE, variableMetadataOutput, dataMatrixOutput, sampleNamesList) {
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229 dataMatrix <- featureValues(xdata, method = "medret", value = intval)
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230 colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix)))
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231 dataMatrix <- cbind(name = groupnames(xdata), dataMatrix)
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232 variableMetadata <- featureDefinitions(xdata)
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233 colnames(variableMetadata)[1] <- "mz"
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234 colnames(variableMetadata)[4] <- "rt"
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235 variableMetadata <- data.frame(name = groupnames(xdata), variableMetadata)
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236
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237 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
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238 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = numDigitsRT, numDigitsMZ = numDigitsMZ)
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239 dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)
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240
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241 # FIX: issue when the vector at peakidx is too long and is written in a new line during the export
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242 variableMetadata[, "peakidx"] <- vapply(variableMetadata[, "peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",")
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243
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244 write.table(variableMetadata, file = variableMetadataOutput, sep = "\t", quote = FALSE, row.names = FALSE)
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245 write.table(dataMatrix, file = dataMatrixOutput, sep = "\t", quote = FALSE, row.names = FALSE)
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246
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247 }
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248
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249 #@author G. Le Corguille
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250 # It allow different of field separators
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251 getDataFrameFromFile <- function(filename, header = TRUE) {
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252 myDataFrame <- read.table(filename, header = header, sep = ";", stringsAsFactors = FALSE)
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253 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header = header, sep = "\t", stringsAsFactors = FALSE)
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254 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header = header, sep = ",", stringsAsFactors = FALSE)
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255 if (ncol(myDataFrame) < 2) {
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256 error_message <- "Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
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257 print(error_message)
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258 stop(error_message)
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259 }
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260 return(myDataFrame)
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261 }
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262
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263 #@author G. Le Corguille
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264 # Draw the BPI and TIC graphics
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265 # colored by sample names or class names
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266 getPlotChromatogram <- function(chrom, xdata, pdfname = "Chromatogram.pdf", aggregationFun = "max") {
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267
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268 if (aggregationFun == "sum")
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269 type <- "Total Ion Chromatograms"
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270 else
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271 type <- "Base Peak Intensity Chromatograms"
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272
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273 adjusted <- "Raw"
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274 if (hasAdjustedRtime(xdata))
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275 adjusted <- "Adjusted"
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276
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277 main <- paste(type, ":", adjusted, "data")
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278
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279 pdf(pdfname, width = 16, height = 10)
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280
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281 # Color by group
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282 if (length(unique(xdata$sample_group)) < 10) {
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283 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
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284 } else {
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285 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
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286 }
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287 if (length(group_colors) > 1) {
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288 names(group_colors) <- unique(xdata$sample_group)
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289 plot(chrom, col = group_colors[chrom$sample_group], main = main, peakType = "none")
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290 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
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291 }
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292
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293 # Color by sample
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294 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main = main, peakType = "none")
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295 legend("topright", legend = xdata@phenoData@data$sample_name, col = rainbow(length(xdata@phenoData@data$sample_name)), cex = 0.8, lty = 1)
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296
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297 dev.off()
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298 }
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299
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300
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301 # Get the polarities from all the samples of a condition
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302 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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303 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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024974037c4e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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304 getSampleMetadata <- function(xdata = NULL, sampleMetadataOutput = "sampleMetadata.tsv") {
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305 cat("Creating the sampleMetadata file...\n")
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306
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307 #Create the sampleMetada dataframe
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308 sampleMetadata <- xdata@phenoData@data
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309 rownames(sampleMetadata) <- NULL
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310 colnames(sampleMetadata) <- c("sample_name", "class")
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311
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312 sampleNamesOrigin <- sampleMetadata$sample_name
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313 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
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314
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315 if (any(duplicated(sampleNamesMakeNames))) {
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316 write("\n\nERROR: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names().\nIn your case, at least two columns after the renaming obtain the same name, thus XCMS will collapse those columns per name.", stderr())
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317 for (sampleName in sampleNamesOrigin) {
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318 write(paste(sampleName, "\t->\t", make.names(sampleName)), stderr())
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319 }
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320 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
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321 }
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322
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323 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
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324 cat("\n\nWARNING: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names()\nIn your case, one or more sample names will be renamed in the sampleMetadata and dataMatrix files:\n")
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325 for (sampleName in sampleNamesOrigin) {
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326 cat(paste(sampleName, "\t->\t", make.names(sampleName), "\n"))
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327 }
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328 }
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329
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330 sampleMetadata$sample_name <- sampleNamesMakeNames
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331
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332
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333 #For each sample file, the following actions are done
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334 for (fileIdx in seq_len(length(fileNames(xdata)))) {
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335 #Check if the file is in the CDF format
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336 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
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337
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338 # If the column isn't exist, with add one filled with NA
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339 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
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340
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341 #Extract the polarity (a list of polarities)
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342 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx, "polarity"]
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343 #Verify if all the scans have the same polarity
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344 uniq_list <- unique(polarity)
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345 if (length(uniq_list) > 1) {
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346 polarity <- "mixed"
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347 } else {
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348 polarity <- as.character(uniq_list)
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349 }
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350
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351 #Set the polarity attribute
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352 sampleMetadata$polarity[fileIdx] <- polarity
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353 }
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354
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355 }
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356
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357 write.table(sampleMetadata, sep = "\t", quote = FALSE, row.names = FALSE, file = sampleMetadataOutput)
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358
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359 return(list("sampleNamesOrigin" = sampleNamesOrigin, "sampleNamesMakeNames" = sampleNamesMakeNames))
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360
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361 }
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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362
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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363
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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364 # This function will compute MD5 checksum to check the data integrity
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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365 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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366 getMd5sum <- function(files) {
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367 cat("Compute md5 checksum...\n")
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368 library(tools)
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369 return(as.matrix(md5sum(files)))
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370 }
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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371
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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372 # This function retrieve the raw file in the working directory
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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373 # - if zipfile: unzip the file with its directory tree
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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374 # - if singlefiles: set symlink with the good filename
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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375 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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024974037c4e "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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376 retrieveRawfileInTheWorkingDir <- function(singlefile, zipfile, args, prefix = "") {
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377
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378 if (!(prefix %in% c("", "Positive", "Negative", "MS1", "MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
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379
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380 # single - if the file are passed in the command arguments -> refresh singlefile
8846a03995d3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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381 if (!is.null(args[[paste0("singlefile_galaxyPath", prefix)]])) {
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382 singlefile_galaxyPaths <- unlist(strsplit(args[[paste0("singlefile_galaxyPath", prefix)]], "\\|"))
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383 singlefile_sampleNames <- unlist(strsplit(args[[paste0("singlefile_sampleName", prefix)]], "\\|"))
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384
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385 singlefile <- NULL
8846a03995d3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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386 for (singlefile_galaxyPath_i in seq_len(length(singlefile_galaxyPaths))) {
8846a03995d3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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387 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
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388 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
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389 # In case, an url is used to import data within Galaxy
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390 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName, "/")), n = 1)
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391 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
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392 }
8846a03995d3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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393 }
8846a03995d3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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394 # zipfile - if the file are passed in the command arguments -> refresh zipfile
8846a03995d3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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395 if (!is.null(args[[paste0("zipfile", prefix)]]))
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396 zipfile <- args[[paste0("zipfile", prefix)]]
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397
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398 # single
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399 if (!is.null(singlefile) && (length("singlefile") > 0)) {
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400 files <- vector()
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401 for (singlefile_sampleName in names(singlefile)) {
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402 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
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403 if (!file.exists(singlefile_galaxyPath)) {
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404 error_message <- paste("Cannot access the sample:", singlefile_sampleName, "located:", singlefile_galaxyPath, ". Please, contact your administrator ... if you have one!")
8846a03995d3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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405 print(error_message)
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406 stop(error_message)
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407 }
0
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408
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409 if (!suppressWarnings(try(file.link(singlefile_galaxyPath, singlefile_sampleName), silent = TRUE)))
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410 file.copy(singlefile_galaxyPath, singlefile_sampleName)
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411 files <- c(files, singlefile_sampleName)
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412 }
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413 }
8846a03995d3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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414 # zipfile
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415 if (!is.null(zipfile) && (zipfile != "")) {
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416 if (!file.exists(zipfile)) {
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417 error_message <- paste("Cannot access the Zip file:", zipfile, ". Please, contact your administrator ... if you have one!")
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418 print(error_message)
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419 stop(error_message)
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420 }
8846a03995d3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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421 suppressWarnings(unzip(zipfile, unzip = "unzip"))
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422
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423 #get the directory name
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424 suppressWarnings(filesInZip <- unzip(zipfile, list = TRUE))
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425 directories <- unique(unlist(lapply(strsplit(filesInZip$Name, "/"), function(x) x[1])))
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426 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
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427 directory <- "."
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428 if (length(directories) == 1) directory <- directories
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429
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430 cat("files_root_directory\t", directory, "\n")
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431
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432 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
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433 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|")
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434 info <- file.info(directory)
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435 listed <- list.files(directory[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE)
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436 files <- c(directory[!info$isdir], listed)
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437 exists <- file.exists(files)
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438 files <- files[exists]
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439
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440 }
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441 return(list(zipfile = zipfile, singlefile = singlefile, files = files))
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442 }
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443
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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444
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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445 # This function retrieve a xset like object
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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446 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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447 getxcmsSetObject <- function(xobject) {
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448 # XCMS 1.x
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449 if (class(xobject) == "xcmsSet")
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450 return(xobject)
8846a03995d3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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451 # XCMS 3.x
8846a03995d3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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452 if (class(xobject) == "XCMSnExp") {
8846a03995d3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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453 # Get the legacy xcmsSet object
8846a03995d3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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454 suppressWarnings(xset <- as(xobject, "xcmsSet"))
8846a03995d3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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455 if (!is.null(xset@phenoData$sample_group))
8846a03995d3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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456 sampclass(xset) <- xset@phenoData$sample_group
8846a03995d3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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457 else
8846a03995d3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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458 sampclass(xset) <- "."
8846a03995d3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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459 return(xset)
8846a03995d3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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460 }
0
c749bfd3410e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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461 }