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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
author workflow4metabolomics
date Mon, 03 Feb 2025 14:43:08 +0000
parents b25a582ab6c1
children
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733d32b30aff planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
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1 # @authors ABiMS TEAM, Y. Guitton
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2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
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4 # @author G. Le Corguille
0
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5 # solve an issue with batch if arguments are logical TRUE/FALSE
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6 parseCommandArgs <- function(...) {
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7 args <- batch::parseCommandArgs(...)
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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 }
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12 }
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13 return(args)
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14 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
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16 # @author G. Le Corguille
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17 # This function will
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18 # - load the packages
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19 # - display the sessionInfo
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20 loadAndDisplayPackages <- function(pkgs) {
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21 for (pkg in pkgs) suppressPackageStartupMessages(stopifnot(library(pkg, quietly = TRUE, logical.return = TRUE, character.only = TRUE)))
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23 sessioninfo <- sessionInfo()
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24 cat(sessioninfo$R.version$version.string, "\n")
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25 cat("Main packages:\n")
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26 for (pkg in names(sessioninfo$otherPkgs)) {
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27 cat(paste(pkg, packageVersion(pkg)), "\t")
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28 }
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29 cat("\n")
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30 cat("Other loaded packages:\n")
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31 for (pkg in names(sessioninfo$loadedOnly)) {
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32 cat(paste(pkg, packageVersion(pkg)), "\t")
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33 }
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34 cat("\n")
0
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35 }
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37 # @author G. Le Corguille
2
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38 # This function merge several chromBPI or chromTIC into one.
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39 mergeChrom <- function(chrom_merged, chrom) {
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40 if (is.null(chrom_merged)) {
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41 return(NULL)
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42 }
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43 chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)
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44 return(chrom_merged)
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45 }
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47 # @author G. Le Corguille
0
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48 # This function merge several xdata into one.
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49 mergeXData <- function(args) {
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50 chromTIC <- NULL
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51 chromBPI <- NULL
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52 chromTIC_adjusted <- NULL
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53 chromBPI_adjusted <- NULL
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54 md5sumList <- NULL
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55 for (image in args$images) {
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56 load(image)
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57 # Handle infiles
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58 if (!exists("singlefile")) singlefile <- NULL
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59 if (!exists("zipfile")) zipfile <- NULL
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60 rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
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61 zipfile <- rawFilePath$zipfile
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62 singlefile <- rawFilePath$singlefile
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64 if (exists("raw_data")) xdata <- raw_data
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65 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
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67 cat(sampleNamesList$sampleNamesOrigin, "\n")
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68
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69 if (!exists("xdata_merged")) {
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70 xdata_merged <- xdata
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71 singlefile_merged <- singlefile
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72 md5sumList_merged <- md5sumList
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73 sampleNamesList_merged <- sampleNamesList
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74 chromTIC_merged <- chromTIC
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75 chromBPI_merged <- chromBPI
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76 chromTIC_adjusted_merged <- chromTIC_adjusted
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77 chromBPI_adjusted_merged <- chromBPI_adjusted
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78 } else {
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79 if (is(xdata, "XCMSnExp")) {
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80 xdata_merged <- c(xdata_merged, xdata)
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81 } else if (is(xdata, "OnDiskMSnExp")) {
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82 xdata_merged <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged, xdata)
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83 } else {
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84 stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
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85 }
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86
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87 singlefile_merged <- c(singlefile_merged, singlefile)
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88 md5sumList_merged$origin <- rbind(md5sumList_merged$origin, md5sumList$origin)
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89 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin, sampleNamesList$sampleNamesOrigin)
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90 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames, sampleNamesList$sampleNamesMakeNames)
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91 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC)
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92 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)
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93 chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)
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94 chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)
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95 }
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96 }
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97 rm(image)
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98 xdata <- xdata_merged
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99 rm(xdata_merged)
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100 singlefile <- singlefile_merged
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101 rm(singlefile_merged)
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102 md5sumList <- md5sumList_merged
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103 rm(md5sumList_merged)
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104 sampleNamesList <- sampleNamesList_merged
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105 rm(sampleNamesList_merged)
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106
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107 if (!is.null(args$sampleMetadata)) {
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108 cat("\tXSET PHENODATA SETTING...\n")
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109 sampleMetadataFile <- args$sampleMetadata
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110 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header = FALSE)
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111 xdata@phenoData@data$sample_group <- sampleMetadata$V2[match(xdata@phenoData@data$sample_name, sampleMetadata$V1)]
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112
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113 if (any(is.na(pData(xdata)$sample_group))) {
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114 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
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115 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse = " "))
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116 print(error_message)
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117 stop(error_message)
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118 }
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119 }
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120
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121 if (!is.null(chromTIC_merged)) {
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122 chromTIC <- chromTIC_merged
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123 chromTIC@phenoData <- xdata@phenoData
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124 }
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125 if (!is.null(chromBPI_merged)) {
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126 chromBPI <- chromBPI_merged
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127 chromBPI@phenoData <- xdata@phenoData
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128 }
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129 if (!is.null(chromTIC_adjusted_merged)) {
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130 chromTIC_adjusted <- chromTIC_adjusted_merged
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131 chromTIC_adjusted@phenoData <- xdata@phenoData
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132 }
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133 if (!is.null(chromBPI_adjusted_merged)) {
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134 chromBPI_adjusted <- chromBPI_adjusted_merged
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135 chromBPI_adjusted@phenoData <- xdata@phenoData
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136 }
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137
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138 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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139 }
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140
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141 # @author G. Le Corguille
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142 # This function convert if it is required the Retention Time in minutes
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143 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
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144 if (convertRTMinute) {
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145 # converting the retention times (seconds) into minutes
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146 print("converting the retention times into minutes in the variableMetadata")
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147 variableMetadata[, "rt"] <- variableMetadata[, "rt"] / 60
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148 variableMetadata[, "rtmin"] <- variableMetadata[, "rtmin"] / 60
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149 variableMetadata[, "rtmax"] <- variableMetadata[, "rtmax"] / 60
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150 }
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151 return(variableMetadata)
0
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152 }
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153
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154 # @author G. Le Corguille
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155 # This function format ions identifiers
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156 formatIonIdentifiers <- function(variableMetadata, numDigitsRT = 0, numDigitsMZ = 0) {
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157 splitDeco <- strsplit(as.character(variableMetadata$name), "_")
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158 idsDeco <- sapply(
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159 splitDeco,
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160 function(x) {
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161 deco <- unlist(x)[2]
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162 if (is.na(deco)) {
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163 return("")
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164 } else {
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165 return(paste0("_", deco))
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166 }
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167 }
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168 )
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169 namecustom <- make.unique(paste0("M", round(variableMetadata[, "mz"], numDigitsMZ), "T", round(variableMetadata[, "rt"], numDigitsRT), idsDeco))
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170 variableMetadata <- cbind(name = variableMetadata$name, namecustom = namecustom, variableMetadata[, !(colnames(variableMetadata) %in% c("name"))])
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171 return(variableMetadata)
0
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172 }
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173
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174 # @author G. Le Corguille
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175 # This function convert the remain NA to 0 in the dataMatrix
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176 naTOzeroDataMatrix <- function(dataMatrix, naTOzero) {
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177 if (naTOzero) {
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178 dataMatrix[is.na(dataMatrix)] <- 0
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179 }
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180 return(dataMatrix)
0
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181 }
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182
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183 # @author G. Le Corguille
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184 # Draw the plotChromPeakDensity 3 per page in a pdf file
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185 getPlotChromPeakDensity <- function(xdata, param = NULL, mzdigit = 4) {
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186 pdf(file = "plotChromPeakDensity.pdf", width = 16, height = 12)
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187
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188 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
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189
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190 if (length(unique(xdata$sample_group)) < 10) {
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191 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
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192 } else {
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193 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
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194 }
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195 names(group_colors) <- unique(xdata$sample_group)
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196 col_per_samp <- as.character(xdata$sample_group)
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197 for (i in seq_len(length(group_colors))) {
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198 col_per_samp[col_per_samp == (names(group_colors)[i])] <- group_colors[i]
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199 }
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200
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201 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
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202 for (i in seq_len(nrow(featureDefinitions(xdata)))) {
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203 mzmin <- featureDefinitions(xdata)[i, ]$mzmin
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204 mzmax <- featureDefinitions(xdata)[i, ]$mzmax
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205 plotChromPeakDensity(xdata, param = param, mz = c(mzmin, mzmax), col = col_per_samp, pch = 16, xlim = xlim, main = paste(round(mzmin, mzdigit), round(mzmax, mzdigit)))
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206 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
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207 }
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208
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209 dev.off()
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210 }
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211
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212 # @author G. Le Corguille
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213 # Draw the plotChromPeakDensity 3 per page in a pdf file
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214 getPlotAdjustedRtime <- function(xdata) {
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215 pdf(file = "raw_vs_adjusted_rt.pdf", width = 16, height = 12)
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216
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217 # Color by group
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218 if (length(unique(xdata$sample_group)) < 10) {
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219 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
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220 } else {
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221 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
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222 }
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223 if (length(group_colors) > 1) {
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224 names(group_colors) <- unique(xdata$sample_group)
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225 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
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226 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
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227 }
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228
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229 # Color by sample
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230 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
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231 legend("topright", legend = xdata@phenoData@data$sample_name, col = rainbow(length(xdata@phenoData@data$sample_name)), cex = 0.8, lty = 1)
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232
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233 dev.off()
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234 }
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235
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236 # @author G. Le Corguille
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237 # value: intensity values to be used into, maxo or intb
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238 getPeaklistW4M <- function(xdata, intval = "into", convertRTMinute = FALSE, numDigitsMZ = 4, numDigitsRT = 0, naTOzero = TRUE, variableMetadataOutput, dataMatrixOutput, sampleNamesList) {
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239 dataMatrix <- featureValues(xdata, method = "medret", value = intval)
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240 colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix)))
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241 dataMatrix <- cbind(name = groupnames(xdata), dataMatrix)
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242 variableMetadata <- featureDefinitions(xdata)
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243 colnames(variableMetadata)[1] <- "mz"
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244 colnames(variableMetadata)[4] <- "rt"
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245 variableMetadata <- data.frame(name = groupnames(xdata), variableMetadata)
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246
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247 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
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248 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = numDigitsRT, numDigitsMZ = numDigitsMZ)
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249 dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)
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250
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251 # FIX: issue when the vector at peakidx is too long and is written in a new line during the export
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252 variableMetadata[, "peakidx"] <- vapply(variableMetadata[, "peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",")
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253
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254 write.table(variableMetadata, file = variableMetadataOutput, sep = "\t", quote = FALSE, row.names = FALSE)
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255 write.table(dataMatrix, file = dataMatrixOutput, sep = "\t", quote = FALSE, row.names = FALSE)
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256 }
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257
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258 # @author G. Le Corguille
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259 # It allow different of field separators
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260 getDataFrameFromFile <- function(filename, header = TRUE) {
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261 myDataFrame <- read.table(filename, header = header, sep = ";", stringsAsFactors = FALSE)
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262 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header = header, sep = "\t", stringsAsFactors = FALSE)
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263 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header = header, sep = ",", stringsAsFactors = FALSE)
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264 if (ncol(myDataFrame) < 2) {
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265 error_message <- "Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
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266 print(error_message)
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267 stop(error_message)
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268 }
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269 return(myDataFrame)
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270 }
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271
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272 # @author G. Le Corguille
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273 # Draw the BPI and TIC graphics
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274 # colored by sample names or class names
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275 getPlotChromatogram <- function(chrom, xdata, pdfname = "Chromatogram.pdf", aggregationFun = "max") {
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276 if (aggregationFun == "sum") {
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277 type <- "Total Ion Chromatograms"
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278 } else {
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279 type <- "Base Peak Intensity Chromatograms"
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280 }
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281
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282 adjusted <- "Raw"
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283 if (hasAdjustedRtime(xdata)) {
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284 adjusted <- "Adjusted"
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285 }
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286
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287 main <- paste(type, ":", adjusted, "data")
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288
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289 pdf(pdfname, width = 16, height = 10)
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290
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291 # Color by group
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292 if (length(unique(xdata$sample_group)) < 10) {
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293 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
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294 } else {
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295 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
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296 }
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297 if (length(group_colors) > 1) {
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298 names(group_colors) <- unique(xdata$sample_group)
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299 plot(chrom, col = group_colors[chrom$sample_group], main = main, peakType = "none")
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300 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
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301 }
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302
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303 # Color by sample
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304 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main = main, peakType = "none")
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305 legend("topright", legend = xdata@phenoData@data$sample_name, col = rainbow(length(xdata@phenoData@data$sample_name)), cex = 0.8, lty = 1)
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306
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307 dev.off()
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308 }
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309
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310
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311 # Get the polarities from all the samples of a condition
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312 # @author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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313 # @author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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314 getSampleMetadata <- function(xdata = NULL, sampleMetadataOutput = "sampleMetadata.tsv") {
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315 cat("Creating the sampleMetadata file...\n")
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316
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317 # Create the sampleMetada dataframe
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318 sampleMetadata <- xdata@phenoData@data
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319 rownames(sampleMetadata) <- NULL
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320 colnames(sampleMetadata) <- c("sample_name", "class")
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321
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322 sampleNamesOrigin <- sampleMetadata$sample_name
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323 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
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324
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325 if (any(duplicated(sampleNamesMakeNames))) {
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326 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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327 for (sampleName in sampleNamesOrigin) {
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328 write(paste(sampleName, "\t->\t", make.names(sampleName)), stderr())
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329 }
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330 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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331 }
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332
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333 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
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334 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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335 for (sampleName in sampleNamesOrigin) {
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336 cat(paste(sampleName, "\t->\t", make.names(sampleName), "\n"))
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337 }
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338 }
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339
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340 sampleMetadata$sample_name <- sampleNamesMakeNames
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341
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342
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343 # For each sample file, the following actions are done
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344 for (fileIdx in seq_len(length(fileNames(xdata)))) {
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345 # Check if the file is in the CDF format
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346 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
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347 # If the column isn't exist, with add one filled with NA
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348 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
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349
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350 # Extract the polarity (a list of polarities)
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351 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx, "polarity"]
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352 # Verify if all the scans have the same polarity
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353 uniq_list <- unique(polarity)
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354 if (length(uniq_list) > 1) {
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355 polarity <- "mixed"
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356 } else {
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357 polarity <- as.character(uniq_list)
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358 }
0
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359
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360 # Set the polarity attribute
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361 sampleMetadata$polarity[fileIdx] <- polarity
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362 }
0
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363 }
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364
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365 write.table(sampleMetadata, sep = "\t", quote = FALSE, row.names = FALSE, file = sampleMetadataOutput)
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366
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367 return(list("sampleNamesOrigin" = sampleNamesOrigin, "sampleNamesMakeNames" = sampleNamesMakeNames))
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368 }
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369
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370
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371 # This function will compute MD5 checksum to check the data integrity
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372 # @author Gildas Le Corguille lecorguille@sb-roscoff.fr
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373 getMd5sum <- function(files) {
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374 cat("Compute md5 checksum...\n")
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375 library(tools)
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376 return(as.matrix(md5sum(files)))
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377 }
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378
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379 # This function retrieve the raw file in the working directory
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380 # - if zipfile: unzip the file with its directory tree
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381 # - if singlefiles: set symlink with the good filename
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382 # @author Gildas Le Corguille lecorguille@sb-roscoff.fr
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383 retrieveRawfileInTheWorkingDir <- function(singlefile, zipfile, args, prefix = "") {
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384 if (!(prefix %in% c("", "Positive", "Negative", "MS1", "MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
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385
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386 # single - if the file are passed in the command arguments -> refresh singlefile
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387 if (!is.null(args[[paste0("singlefile_galaxyPath", prefix)]])) {
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388 singlefile_galaxyPaths <- unlist(strsplit(args[[paste0("singlefile_galaxyPath", prefix)]], "\\|"))
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389 singlefile_sampleNames <- unlist(strsplit(args[[paste0("singlefile_sampleName", prefix)]], "\\|"))
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390
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391 singlefile <- NULL
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392 for (singlefile_galaxyPath_i in seq_len(length(singlefile_galaxyPaths))) {
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393 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
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394 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
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395 # In case, an url is used to import data within Galaxy
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396 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName, "/")), n = 1)
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397 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
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398 }
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399 }
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400 # zipfile - if the file are passed in the command arguments -> refresh zipfile
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401 if (!is.null(args[[paste0("zipfile", prefix)]])) {
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402 zipfile <- args[[paste0("zipfile", prefix)]]
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403 }
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404
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405 # single
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406 if (!is.null(singlefile) && (length("singlefile") > 0)) {
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407 files <- vector()
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408 for (singlefile_sampleName in names(singlefile)) {
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409 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
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410 if (!file.exists(singlefile_galaxyPath)) {
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411 error_message <- paste("Cannot access the sample:", singlefile_sampleName, "located:", singlefile_galaxyPath, ". Please, contact your administrator ... if you have one!")
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412 print(error_message)
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413 stop(error_message)
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414 }
0
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415
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416 if (!suppressWarnings(try(file.link(singlefile_galaxyPath, singlefile_sampleName), silent = TRUE))) {
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417 file.copy(singlefile_galaxyPath, singlefile_sampleName)
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418 }
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419 files <- c(files, singlefile_sampleName)
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420 }
0
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421 }
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422 # zipfile
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423 if (!is.null(zipfile) && (zipfile != "")) {
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424 if (!file.exists(zipfile)) {
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425 error_message <- paste("Cannot access the Zip file:", zipfile, ". Please, contact your administrator ... if you have one!")
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426 print(error_message)
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427 stop(error_message)
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428 }
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429 suppressWarnings(unzip(zipfile, unzip = "unzip"))
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430
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431 # get the directory name
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432 suppressWarnings(filesInZip <- unzip(zipfile, list = TRUE))
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433 directories <- unique(unlist(lapply(strsplit(filesInZip$Name, "/"), function(x) x[1])))
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434 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
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435 directory <- "."
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436 if (length(directories) == 1) directory <- directories
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437
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438 cat("files_root_directory\t", directory, "\n")
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439
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440 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
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441 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|")
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442 info <- file.info(directory)
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443 listed <- list.files(directory[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE)
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444 files <- c(directory[!info$isdir], listed)
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445 exists <- file.exists(files)
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446 files <- files[exists]
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447 }
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448 return(list(zipfile = zipfile, singlefile = singlefile, files = files))
0
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449 }
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450
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451
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452 # This function retrieve a xset like object
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453 # @author Gildas Le Corguille lecorguille@sb-roscoff.fr
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454 getxcmsSetObject <- function(xobject) {
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455 # XCMS 1.x
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456 if (class(xobject) == "xcmsSet") {
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457 return(xobject)
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458 }
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459 # XCMS 3.x
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460 if (class(xobject) == "XCMSnExp") {
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461 # Get the legacy xcmsSet object
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462 suppressWarnings(xset <- as(xobject, "xcmsSet"))
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463 if (!is.null(xset@phenoData$sample_group)) {
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464 sampclass(xset) <- xset@phenoData$sample_group
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465 } else {
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466 sampclass(xset) <- "."
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467 }
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468 return(xset)
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469 }
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470 }