Mercurial > repos > lecorguille > xcms_xcmsset

annotate lib.r @ 33:c363b9f1caef draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
author lecorguille
date Mon, 05 Mar 2018 04:15:34 -0500
parents 2bf1cb023c94
children efd23113d5f4
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2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
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1 #@authors ABiMS TEAM, Y. Guitton
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
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2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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4 #@author G. Le Corguille
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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5 # solve an issue with batch if arguments are logical TRUE/FALSE
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
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6 parseCommandArgs <- function(...) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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7 args <- batch::parseCommandArgs(...)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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8 for (key in names(args)) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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9 if (args[key] %in% c("TRUE","FALSE"))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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10 args[key] = as.logical(args[key])
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11 }
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12 return(args)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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13 }
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f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
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15 #@author G. Le Corguille
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16 # This function will
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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17 # - load the packages
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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18 # - display the sessionInfo
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19 loadAndDisplayPackages <- function(pkgs) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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20 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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22 sessioninfo = sessionInfo()
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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23 cat(sessioninfo$R.version$version.string,"\n")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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24 cat("Main packages:\n")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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26 cat("Other loaded packages:\n")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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28 }
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30 #@author G. Le Corguille
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lecorguille
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31 # This function convert if it is required the Retention Time in minutes
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32 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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33 if (convertRTMinute){
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
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34 #converting the retention times (seconds) into minutes
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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35 print("converting the retention times into minutes in the variableMetadata")
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36 variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60
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37 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60
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38 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60
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39 }
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40 return (variableMetadata)
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41 }
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43 #@author G. Le Corguille
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44 # This function format ions identifiers
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45 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
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46 splitDeco <- strsplit(as.character(variableMetadata$name),"_")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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47 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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48 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
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49 variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
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50 return(variableMetadata)
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51 }
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53 #@author G. Le Corguille
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54 # Draw the plotChromPeakDensity 3 per page in a pdf file
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55 getPlotChromPeakDensity <- function(xdata, mzdigit=4) {
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56 pdf(file="plotChromPeakDensity.pdf", width=16, height=12)
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58 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
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60 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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61 names(group_colors) <- unique(xdata$sample_group)
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63 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
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64 for (i in 1:nrow(featureDefinitions(xdata))) {
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65 mzmin = featureDefinitions(xdata)[i,]$mzmin
c363b9f1caef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
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66 mzmax = featureDefinitions(xdata)[i,]$mzmax
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67 plotChromPeakDensity(xdata, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
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68 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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69 }
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71 dev.off()
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72 }
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74 #@author G. Le Corguille
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lecorguille
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75 # Draw the plotChromPeakDensity 3 per page in a pdf file
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76 getPlotAdjustedRtime <- function(xdata) {
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77 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
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lecorguille
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78 # Color by group
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lecorguille
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79 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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80 names(group_colors) <- unique(xdata$sample_group)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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81 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
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82 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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83 # Color by sample
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84 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
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85 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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86 dev.off()
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87 }
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89 #@author G. Le Corguille
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90 # value: intensity values to be used into, maxo or intb
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91 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, variableMetadataOutput, dataMatrixOutput) {
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92 dataMatrix <- featureValues(xdata, method="medret", value=intval)
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93 colnames(dataMatrix) <- tools::file_path_sans_ext(colnames(dataMatrix))
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94 dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix)
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95 variableMetadata <- featureDefinitions(xdata)
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96 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
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97 variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata)
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98
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99 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
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100 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
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101
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102 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
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103 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
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104
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105 }
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106
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107 #@author Y. Guitton
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108 getBPC <- function(file,rtcor=NULL, ...) {
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109 object <- xcmsRaw(file)
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110 sel <- profRange(object, ...)
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111 cbind(if (is.null(rtcor)) object@scantime[sel$scanidx] else rtcor ,xcms:::colMax(object@env$profile[sel$massidx,sel$scanidx,drop=FALSE]))
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112 #plotChrom(xcmsRaw(file), base=T)
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113 }
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114
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115 #@author Y. Guitton
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116 getBPCs <- function (xcmsSet=NULL, pdfname="BPCs.pdf",rt=c("raw","corrected"), scanrange=NULL) {
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117 cat("Creating BIC pdf...\n")
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118
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119 if (is.null(xcmsSet)) {
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120 cat("Enter an xcmsSet \n")
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121 stop()
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122 } else {
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123 files <- filepaths(xcmsSet)
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124 }
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125
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126 phenoDataClass <- as.vector(levels(xcmsSet@phenoData[,"class"])) #sometime phenoData have more than 1 column use first as class
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127
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128 classnames <- vector("list",length(phenoDataClass))
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129 for (i in 1:length(phenoDataClass)){
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130 classnames[[i]] <- which( xcmsSet@phenoData[,"class"]==phenoDataClass[i])
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131 }
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132
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133 N <- dim(phenoData(xcmsSet))[1]
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134
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135 TIC <- vector("list",N)
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136
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137
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138 for (j in 1:N) {
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139
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140 TIC[[j]] <- getBPC(files[j])
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141 #good for raw
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142 # seems strange for corrected
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143 #errors if scanrange used in xcmsSetgeneration
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144 if (!is.null(xcmsSet) && rt == "corrected")
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145 rtcor <- xcmsSet@rt$corrected[[j]]
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146 else
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147 rtcor <- NULL
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148
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149 TIC[[j]] <- getBPC(files[j],rtcor=rtcor)
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150 # TIC[[j]][,1]<-rtcor
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151 }
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152
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153
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154
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155 pdf(pdfname,w=16,h=10)
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156 cols <- rainbow(N)
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157 lty <- 1:N
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158 pch <- 1:N
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159 #search for max x and max y in BPCs
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160 xlim <- range(sapply(TIC, function(x) range(x[,1])))
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161 ylim <- range(sapply(TIC, function(x) range(x[,2])))
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162 ylim <- c(-ylim[2], ylim[2])
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163
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164
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165 ##plot start
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166
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167 if (length(phenoDataClass)>2){
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168 for (k in 1:(length(phenoDataClass)-1)){
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169 for (l in (k+1):length(phenoDataClass)){
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170 #print(paste(phenoDataClass[k],"vs",phenoDataClass[l],sep=" "))
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171 plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k]," vs ",phenoDataClass[l], sep=""), xlab="Retention Time (min)", ylab="BPC")
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172 colvect <- NULL
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173 for (j in 1:length(classnames[[k]])) {
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174 tic <- TIC[[classnames[[k]][j]]]
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175 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
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176 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
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177 colvect <- append(colvect,cols[classnames[[k]][j]])
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178 }
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179 for (j in 1:length(classnames[[l]])) {
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180 # i <- class2names[j]
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181 tic <- TIC[[classnames[[l]][j]]]
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182 points(tic[,1]/60, -tic[,2], col=cols[classnames[[l]][j]], pch=pch[classnames[[l]][j]], type="l")
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183 colvect <- append(colvect,cols[classnames[[l]][j]])
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184 }
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185 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col=colvect, lty=lty, pch=pch)
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186 }
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187 }
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188 }#end if length >2
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189
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190 if (length(phenoDataClass)==2){
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191 k <- 1
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192 l <- 2
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193 colvect <- NULL
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194 plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k],"vs",phenoDataClass[l], sep=""), xlab="Retention Time (min)", ylab="BPC")
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195
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196 for (j in 1:length(classnames[[k]])) {
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198 tic <- TIC[[classnames[[k]][j]]]
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199 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
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200 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
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201 colvect<-append(colvect,cols[classnames[[k]][j]])
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202 }
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203 for (j in 1:length(classnames[[l]])) {
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204 # i <- class2names[j]
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205 tic <- TIC[[classnames[[l]][j]]]
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206 points(tic[,1]/60, -tic[,2], col=cols[classnames[[l]][j]], pch=pch[classnames[[l]][j]], type="l")
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207 colvect <- append(colvect,cols[classnames[[l]][j]])
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208 }
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209 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col=colvect, lty=lty, pch=pch)
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210
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211 }#end length ==2
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212
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213 #case where only one class
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214 if (length(phenoDataClass)==1){
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215 k <- 1
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216 ylim <- range(sapply(TIC, function(x) range(x[,2])))
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217 colvect <- NULL
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218 plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k], sep=""), xlab="Retention Time (min)", ylab="BPC")
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219
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220 for (j in 1:length(classnames[[k]])) {
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221 tic <- TIC[[classnames[[k]][j]]]
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222 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
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223 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
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224 colvect <- append(colvect,cols[classnames[[k]][j]])
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225 }
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226
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227 legend("topright",paste(basename(files[c(classnames[[k]])])), col=colvect, lty=lty, pch=pch)
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228
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229 }#end length ==1
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230
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231 dev.off() #pdf(pdfname,w=16,h=10)
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232
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233 invisible(TIC)
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234 }
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235
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236
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237
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238 #@author Y. Guitton
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239 getTIC <- function(file, rtcor=NULL) {
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240 object <- xcmsRaw(file)
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241 cbind(if (is.null(rtcor)) object@scantime else rtcor, rawEIC(object, mzrange=range(object@env$mz))$intensity)
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242 }
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243
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244 #overlay TIC from all files in current folder or from xcmsSet, create pdf
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245 #@author Y. Guitton
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246 getTICs <- function(xcmsSet=NULL,files=NULL, pdfname="TICs.pdf", rt=c("raw","corrected")) {
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247 cat("Creating TIC pdf...\n")
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248
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249 if (is.null(xcmsSet)) {
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250 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
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251 filepattern <- paste(paste("\\.", filepattern, "$", sep=""), collapse="|")
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252 if (is.null(files))
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253 files <- getwd()
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254 info <- file.info(files)
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255 listed <- list.files(files[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
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256 files <- c(files[!info$isdir], listed)
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257 } else {
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258 files <- filepaths(xcmsSet)
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259 }
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260
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261 phenoDataClass <- as.vector(levels(xcmsSet@phenoData[,"class"])) #sometime phenoData have more than 1 column use first as class
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262 classnames <- vector("list",length(phenoDataClass))
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263 for (i in 1:length(phenoDataClass)){
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264 classnames[[i]] <- which( xcmsSet@phenoData[,"class"]==phenoDataClass[i])
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265 }
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266
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267 N <- length(files)
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268 TIC <- vector("list",N)
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269
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270 for (i in 1:N) {
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271 if (!is.null(xcmsSet) && rt == "corrected")
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272 rtcor <- xcmsSet@rt$corrected[[i]] else
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273 rtcor <- NULL
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274 TIC[[i]] <- getTIC(files[i], rtcor=rtcor)
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275 }
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276
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277 pdf(pdfname, w=16, h=10)
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278 cols <- rainbow(N)
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279 lty <- 1:N
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280 pch <- 1:N
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281 #search for max x and max y in TICs
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282 xlim <- range(sapply(TIC, function(x) range(x[,1])))
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283 ylim <- range(sapply(TIC, function(x) range(x[,2])))
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284 ylim <- c(-ylim[2], ylim[2])
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285
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286
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287 ##plot start
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288 if (length(phenoDataClass)>2){
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289 for (k in 1:(length(phenoDataClass)-1)){
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290 for (l in (k+1):length(phenoDataClass)){
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291 #print(paste(phenoDataClass[k],"vs",phenoDataClass[l],sep=" "))
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292 plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k]," vs ",phenoDataClass[l], sep=""), xlab="Retention Time (min)", ylab="TIC")
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293 colvect <- NULL
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294 for (j in 1:length(classnames[[k]])) {
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295 tic <- TIC[[classnames[[k]][j]]]
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296 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
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297 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
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298 colvect <- append(colvect,cols[classnames[[k]][j]])
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299 }
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300 for (j in 1:length(classnames[[l]])) {
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301 # i=class2names[j]
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302 tic <- TIC[[classnames[[l]][j]]]
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303 points(tic[,1]/60, -tic[,2], col=cols[classnames[[l]][j]], pch=pch[classnames[[l]][j]], type="l")
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304 colvect <- append(colvect,cols[classnames[[l]][j]])
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305 }
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306 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col=colvect, lty=lty, pch=pch)
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307 }
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308 }
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309 }#end if length >2
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310 if (length(phenoDataClass)==2){
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311 k <- 1
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312 l <- 2
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313
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314 plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k],"vs",phenoDataClass[l], sep=""), xlab="Retention Time (min)", ylab="TIC")
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315 colvect <- NULL
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316 for (j in 1:length(classnames[[k]])) {
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317 tic <- TIC[[classnames[[k]][j]]]
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318 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
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319 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
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320 colvect <- append(colvect,cols[classnames[[k]][j]])
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321 }
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322 for (j in 1:length(classnames[[l]])) {
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323 # i <- class2names[j]
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324 tic <- TIC[[classnames[[l]][j]]]
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325 points(tic[,1]/60, -tic[,2], col=cols[classnames[[l]][j]], pch=pch[classnames[[l]][j]], type="l")
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326 colvect <- append(colvect,cols[classnames[[l]][j]])
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327 }
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328 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col=colvect, lty=lty, pch=pch)
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329
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330 }#end length ==2
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331
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332 #case where only one class
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333 if (length(phenoDataClass)==1){
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334 k <- 1
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335 ylim <- range(sapply(TIC, function(x) range(x[,2])))
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336
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337 plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k], sep=""), xlab="Retention Time (min)", ylab="TIC")
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338 colvect <- NULL
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339 for (j in 1:length(classnames[[k]])) {
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340 tic <- TIC[[classnames[[k]][j]]]
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341 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
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342 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
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343 colvect <- append(colvect,cols[classnames[[k]][j]])
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344 }
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345
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346 legend("topright",paste(basename(files[c(classnames[[k]])])), col=colvect, lty=lty, pch=pch)
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347
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348 }#end length ==1
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349
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350 dev.off() #pdf(pdfname,w=16,h=10)
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351
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352 invisible(TIC)
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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 # Get the polarities from all the samples of a condition
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358 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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359 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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360 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
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361 cat("Creating the sampleMetadata file...\n")
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362
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363 #Create the sampleMetada dataframe
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364 sampleMetadata <- xdata@phenoData@data
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365 rownames(sampleMetadata) <- NULL
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366 colnames(sampleMetadata) <- c("sampleMetadata", "class")
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367
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368 sampleNamesOrigin <- sampleMetadata$sampleMetadata
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369 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
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370
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371 if (any(duplicated(sampleNamesMakeNames))) {
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372 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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373 for (sampleName in sampleNamesOrigin) {
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374 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
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375 }
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376 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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377 }
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378
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379 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
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380 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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381 for (sampleName in sampleNamesOrigin) {
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382 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
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383 }
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384 }
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385
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386 sampleMetadata$sampleMetadata <- sampleNamesMakeNames
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387
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388
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389 #For each sample file, the following actions are done
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390 for (fileIdx in 1:length(fileNames(xdata))) {
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391 #Check if the file is in the CDF format
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392 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
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393
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394 # If the column isn't exist, with add one filled with NA
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395 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
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396
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397 #Extract the polarity (a list of polarities)
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398 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
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399 #Verify if all the scans have the same polarity
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400 uniq_list <- unique(polarity)
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401 if (length(uniq_list)>1){
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402 polarity <- "mixed"
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403 } else {
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404 polarity <- as.character(uniq_list)
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405 }
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406
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407 #Set the polarity attribute
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408 sampleMetadata$polarity[fileIdx] <- polarity
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409 }
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410
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411 }
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412
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413 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
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414
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415 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
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416
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417 }
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418
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419
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420 # This function check if xcms will found all the files
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421 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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422 checkFilesCompatibilityWithXcms <- function(directory) {
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423 cat("Checking files filenames compatibilities with xmcs...\n")
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424 # WHAT XCMS WILL FIND
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425 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
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426 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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427 info <- file.info(directory)
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428 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
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429 files <- c(directory[!info$isdir], listed)
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430 files_abs <- file.path(getwd(), files)
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431 exists <- file.exists(files_abs)
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432 files[exists] <- files_abs[exists]
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433 files[exists] <- sub("//","/",files[exists])
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434
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435 # WHAT IS ON THE FILESYSTEM
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436 filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T)
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437 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
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438
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439 # COMPARISON
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440 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
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441 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
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442 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
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443 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
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444 }
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445 }
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446
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447
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448 #This function list the compatible files within the directory as xcms did
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449 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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450 getMSFiles <- function (directory) {
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451 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
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452 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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453 info <- file.info(directory)
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454 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
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455 files <- c(directory[!info$isdir], listed)
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456 exists <- file.exists(files)
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457 files <- files[exists]
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458 return(files)
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459 }
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460
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461 # This function check if XML contains special caracters. It also checks integrity and completness.
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462 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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463 checkXmlStructure <- function (directory) {
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464 cat("Checking XML structure...\n")
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465
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466 cmd <- paste0("IFS=$'\n'; for xml in $(find '",directory,"' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;")
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467 capture <- system(cmd, intern=TRUE)
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468
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469 if (length(capture)>0){
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470 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
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471 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
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472 write(capture, stderr())
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473 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
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474 }
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475
5
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476 }
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477
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478
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479 # This function check if XML contain special characters
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480 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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481 deleteXmlBadCharacters<- function (directory) {
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482 cat("Checking Non ASCII characters in the XML...\n")
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483
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484 processed <- F
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485 l <- system( paste0("find '",directory, "' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"), intern=TRUE)
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486 for (i in l){
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2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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487 cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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488 capture <- suppressWarnings(system(cmd, intern=TRUE))
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489 if (length(capture)>0){
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490 cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
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491 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
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492 c <- system(cmd, intern=TRUE)
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493 capture <- ""
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494 processed <- T
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495 }
5
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496 }
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497 if (processed) cat("\n\n")
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498 return(processed)
5
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499 }
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500
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501
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502 # This function will compute MD5 checksum to check the data integrity
5
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503 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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504 getMd5sum <- function (directory) {
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505 cat("Compute md5 checksum...\n")
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506 # WHAT XCMS WILL FIND
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507 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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508 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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509 info <- file.info(directory)
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510 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
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511 files <- c(directory[!info$isdir], listed)
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512 exists <- file.exists(files)
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513 files <- files[exists]
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514
17
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515 library(tools)
5
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516
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517 #cat("\n\n")
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518
17
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519 return(as.matrix(md5sum(files)))
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520 }
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diff changeset
521
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522
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523 # This function get the raw file path from the arguments
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524 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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525 getRawfilePathFromArguments <- function(singlefile, zipfile, args) {
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526 if (!is.null(args$zipfile)) zipfile <- args$zipfile
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527 if (!is.null(args$zipfilePositive)) zipfile <- args$zipfilePositive
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528 if (!is.null(args$zipfileNegative)) zipfile <- args$zipfileNegative
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529
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530 if (!is.null(args$singlefile_galaxyPath)) {
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531 singlefile_galaxyPaths <- args$singlefile_galaxyPath;
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532 singlefile_sampleNames <- args$singlefile_sampleName
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533 }
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534 if (!is.null(args$singlefile_galaxyPathPositive)) {
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535 singlefile_galaxyPaths <- args$singlefile_galaxyPathPositive;
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536 singlefile_sampleNames <- args$singlefile_sampleNamePositive
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537 }
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538 if (!is.null(args$singlefile_galaxyPathNegative)) {
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539 singlefile_galaxyPaths <- args$singlefile_galaxyPathNegative;
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540 singlefile_sampleNames <- args$singlefile_sampleNameNegative
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541 }
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542 if (exists("singlefile_galaxyPaths")){
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543 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\|"))
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544 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\|"))
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545
32
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546 singlefile <- NULL
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547 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
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548 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
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549 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
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550 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
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551 }
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552 }
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553 for (argument in c("zipfile","zipfilePositive","zipfileNegative","singlefile_galaxyPath","singlefile_sampleName","singlefile_galaxyPathPositive","singlefile_sampleNamePositive","singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) {
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2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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554 args[[argument]] <- NULL
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diff changeset
555 }
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556 return(list(zipfile=zipfile, singlefile=singlefile, args=args))
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parents: 21
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557 }
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lecorguille
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diff changeset
558
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559
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parents: 21
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560 # This function retrieve the raw file in the working directory
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561 # - if zipfile: unzip the file with its directory tree
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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562 # - if singlefiles: set symlink with the good filename
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563 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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564 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
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diff changeset
565 if(!is.null(singlefile) && (length("singlefile")>0)) {
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
566 for (singlefile_sampleName in names(singlefile)) {
32
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
567 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
24
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
568 if(!file.exists(singlefile_galaxyPath)){
32
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
569 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
24
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
570 print(error_message); stop(error_message)
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
571 }
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
572
32
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
573 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
574 file.copy(singlefile_galaxyPath, singlefile_sampleName)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
575
24
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
576 }
32
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
577 directory <- "."
24
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
578
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
579 }
32
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
580 if(!is.null(zipfile) && (zipfile != "")) {
24
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
581 if(!file.exists(zipfile)){
32
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
582 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
24
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
583 print(error_message)
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
584 stop(error_message)
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
585 }
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
586
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
587 #list all file in the zip file
32
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
588 #zip_files <- unzip(zipfile,list=T)[,"Name"]
24
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
589
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
590 #unzip
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
591 suppressWarnings(unzip(zipfile, unzip="unzip"))
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
592
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
593 #get the directory name
32
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
594 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
595 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
596 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
597 directory <- "."
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
598 if (length(directories) == 1) directory <- directories
24
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
599
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
600 cat("files_root_directory\t",directory,"\n")
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
601
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
602 }
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
603 return (directory)
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
604 }
32
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
605
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
606
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
607 # This function retrieve a xset like object
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
608 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
609 getxcmsSetObject <- function(xobject) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
610 # XCMS 1.x
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
611 if (class(xobject) == "xcmsSet")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
612 return (xobject)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
613 # XCMS 3.x
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
614 if (class(xobject) == "XCMSnExp") {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
615 # Get the legacy xcmsSet object
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
616 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
617 sampclass(xset) <- xset@phenoData$sample_group
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
618 return (xset)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
619 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
620 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
621
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
622
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
623 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
624 # https://github.com/sneumann/xcms/issues/250
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
625 groupnamesW4M <- function(xdata, mzdec = 0, rtdec = 0) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
626 mzfmt <- paste("%.", mzdec, "f", sep = "")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
627 rtfmt <- paste("%.", rtdec, "f", sep = "")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
628
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
629 gnames <- paste("M", sprintf(mzfmt, featureDefinitions(xdata)[,"mzmed"]), "T",
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
630 sprintf(rtfmt, featureDefinitions(xdata)[,"rtmed"]), sep = "")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
631
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
632 if (any(dup <- duplicated(gnames)))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
633 for (dupname in unique(gnames[dup])) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
634 dupidx <- which(gnames == dupname)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
635 gnames[dupidx] <- paste(gnames[dupidx], seq(along = dupidx), sep = "_")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
636 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
637
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
638 return (gnames)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
639 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
640
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
641 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
642 # https://github.com/sneumann/xcms/issues/247
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
643 .concatenate_XCMSnExp <- function(...) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
644 x <- list(...)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
645 if (length(x) == 0)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
646 return(NULL)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
647 if (length(x) == 1)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
648 return(x[[1]])
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
649 ## Check that all are XCMSnExp objects.
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
650 if (!all(unlist(lapply(x, function(z) is(z, "XCMSnExp")))))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
651 stop("All passed objects should be 'XCMSnExp' objects")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
652 new_x <- as(.concatenate_OnDiskMSnExp(...), "XCMSnExp")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
653 ## If any of the XCMSnExp has alignment results or detected features drop
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
654 ## them!
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
655 x <- lapply(x, function(z) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
656 if (hasAdjustedRtime(z)) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
657 z <- dropAdjustedRtime(z)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
658 warning("Adjusted retention times found, had to drop them.")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
659 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
660 if (hasFeatures(z)) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
661 z <- dropFeatureDefinitions(z)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
662 warning("Feature definitions found, had to drop them.")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
663 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
664 z
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
665 })
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
666 ## Combine peaks
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
667 fls <- lapply(x, fileNames)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
668 startidx <- cumsum(lengths(fls))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
669 pks <- lapply(x, chromPeaks)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
670 procH <- lapply(x, processHistory)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
671 for (i in 2:length(fls)) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
672 pks[[i]][, "sample"] <- pks[[i]][, "sample"] + startidx[i - 1]
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
673 procH[[i]] <- lapply(procH[[i]], function(z) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
674 z@fileIndex <- as.integer(z@fileIndex + startidx[i - 1])
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
675 z
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
676 })
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
677 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
678 pks <- do.call(rbind, pks)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
679 new_x@.processHistory <- unlist(procH)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
680 chromPeaks(new_x) <- pks
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
681 if (validObject(new_x))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
682 new_x
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
683 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
684
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
685 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
686 # https://github.com/sneumann/xcms/issues/247
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
687 .concatenate_OnDiskMSnExp <- function(...) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
688 x <- list(...)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
689 if (length(x) == 0)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
690 return(NULL)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
691 if (length(x) == 1)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
692 return(x[[1]])
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
693 ## Check that all are XCMSnExp objects.
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
694 if (!all(unlist(lapply(x, function(z) is(z, "OnDiskMSnExp")))))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
695 stop("All passed objects should be 'OnDiskMSnExp' objects")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
696 ## Check processingQueue
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
697 procQ <- lapply(x, function(z) z@spectraProcessingQueue)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
698 new_procQ <- procQ[[1]]
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
699 is_ok <- unlist(lapply(procQ, function(z)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
700 !is.character(all.equal(new_procQ, z))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
701 ))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
702 if (any(!is_ok)) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
703 warning("Processing queues from the submitted objects differ! ",
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
704 "Dropping the processing queue.")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
705 new_procQ <- list()
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
706 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
707 ## processingData
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
708 fls <- lapply(x, function(z) z@processingData@files)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
709 startidx <- cumsum(lengths(fls))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
710 ## featureData
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
711 featd <- lapply(x, fData)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
712 ## Have to update the file index and the spectrum names.
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
713 for (i in 2:length(featd)) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
714 featd[[i]]$fileIdx <- featd[[i]]$fileIdx + startidx[i - 1]
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
715 rownames(featd[[i]]) <- MSnbase:::formatFileSpectrumNames(
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
716 fileIds = featd[[i]]$fileIdx,
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
717 spectrumIds = featd[[i]]$spIdx,
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
718 nSpectra = nrow(featd[[i]]),
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
719 nFiles = length(unlist(fls))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
720 )
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
721 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
722 featd <- do.call(rbind, featd)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
723 featd$spectrum <- 1:nrow(featd)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
724 ## experimentData
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
725 expdata <- lapply(x, function(z) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
726 ed <- z@experimentData
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
727 data.frame(instrumentManufacturer = ed@instrumentManufacturer,
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
728 instrumentModel = ed@instrumentModel,
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
729 ionSource = ed@ionSource,
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
730 analyser = ed@analyser,
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
731 detectorType = ed@detectorType,
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
732 stringsAsFactors = FALSE)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
733 })
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
734 expdata <- do.call(rbind, expdata)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
735 expdata <- new("MIAPE",
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
736 instrumentManufacturer = expdata$instrumentManufacturer,
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
737 instrumentModel = expdata$instrumentModel,
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
738 ionSource = expdata$ionSource,
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
739 analyser = expdata$analyser,
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
740 detectorType = expdata$detectorType)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
741
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
742 ## protocolData
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
743 protodata <- lapply(x, function(z) z@protocolData)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
744 if (any(unlist(lapply(protodata, nrow)) > 0))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
745 warning("Found non-empty protocol data, but merging protocol data is",
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
746 " currently not supported. Skipped.")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
747 ## phenoData
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
748 pdata <- do.call(rbind, lapply(x, pData))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
749 res <- new(
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
750 "OnDiskMSnExp",
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
751 phenoData = new("NAnnotatedDataFrame", data = pdata),
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
752 featureData = new("AnnotatedDataFrame", featd),
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
753 processingData = new("MSnProcess",
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
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754 processing = paste0("Concatenated [", date(), "]"),
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
755 files = unlist(fls), smoothed = NA),
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
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756 experimentData = expdata,
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
757 spectraProcessingQueue = new_procQ)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
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758 if (validObject(res))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
759 res
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
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760 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
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761
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
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762 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
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763 # https://github.com/sneumann/xcms/issues/247
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
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764 c.XCMSnExp <- function(...) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
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765 .concatenate_XCMSnExp(...)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
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766 }