Mercurial > repos > lecorguille > xcms_xcmsset

annotate lib.r @ 38:e66eeca443e4 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
author lecorguille
date Wed, 05 Sep 2018 05:56:32 -0400
parents 9ada611dd63f
children e8d7395a70b2
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2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
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
parents: 31
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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
parents: 31
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7 args <- batch::parseCommandArgs(...)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
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8 for (key in names(args)) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
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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])
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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11 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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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
lecorguille
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17 # - load the packages
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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18 # - display the sessionInfo
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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19 loadAndDisplayPackages <- function(pkgs) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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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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2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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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
lecorguille
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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$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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26 cat("Other loaded packages:\n")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
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28 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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30 #@author G. Le Corguille
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31 # This function merge several chromBPI or chromTIC into one.
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lecorguille
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32 mergeChrom <- function(chrom_merged, chrom) {
e66eeca443e4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
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33 if (is.null(chrom_merged)) return(NULL)
e66eeca443e4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
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34 chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)
e66eeca443e4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
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35 return(chrom_merged)
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36 }
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38 #@author G. Le Corguille
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39 # This function merge several xdata into one.
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40 mergeXData <- function(args) {
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e66eeca443e4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
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41 chromTIC <- NULL
e66eeca443e4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
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42 chromBPI <- NULL
e66eeca443e4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 37
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43 chromTIC_adjusted <- NULL
e66eeca443e4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
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44 chromBPI_adjusted <- NULL
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45 for(image in args$images) {
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47 load(image)
7f636ad1162b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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48 # Handle infiles
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lecorguille
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49 if (!exists("singlefile")) singlefile <- NULL
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50 if (!exists("zipfile")) zipfile <- NULL
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51 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
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52 zipfile <- rawFilePath$zipfile
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53 singlefile <- rawFilePath$singlefile
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54 retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
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55
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56 if (exists("raw_data")) xdata <- raw_data
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57 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
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58
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59 cat(sampleNamesList$sampleNamesOrigin,"\n")
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60
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61 if (!exists("xdata_merged")) {
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62 xdata_merged <- xdata
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lecorguille
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63 singlefile_merged <- singlefile
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lecorguille
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64 md5sumList_merged <- md5sumList
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65 sampleNamesList_merged <- sampleNamesList
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66 chromTIC_merged <- chromTIC
d39b9aff9cf7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
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67 chromBPI_merged <- chromBPI
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68 chromTIC_adjusted_merged <- chromTIC_adjusted
e66eeca443e4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
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69 chromBPI_adjusted_merged <- chromBPI_adjusted
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70 } else {
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71 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata)
7f636ad1162b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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72 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata)
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73 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
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74
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75 singlefile_merged <- c(singlefile_merged,singlefile)
7f636ad1162b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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76 md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin)
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77 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin)
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78 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames)
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79 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC)
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lecorguille
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80 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)
e66eeca443e4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
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81 chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)
e66eeca443e4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
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82 chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)
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83 }
7f636ad1162b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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84 }
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85 rm(image)
7f636ad1162b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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86 xdata <- xdata_merged; rm(xdata_merged)
7f636ad1162b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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87 singlefile <- singlefile_merged; rm(singlefile_merged)
7f636ad1162b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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88 md5sumList <- md5sumList_merged; rm(md5sumList_merged)
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89 sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
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90
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91 if (!is.null(args$sampleMetadata)) {
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92 cat("\tXSET PHENODATA SETTING...\n")
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93 sampleMetadataFile <- args$sampleMetadata
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94 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header=F)
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95 xdata@phenoData@data$sample_group=sampleMetadata$V2[match(xdata@phenoData@data$sample_name,sampleMetadata$V1)]
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96
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97 if (any(is.na(pData(xdata)$sample_group))) {
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98 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
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99 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" "))
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100 print(error_message)
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101 stop(error_message)
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102 }
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103 }
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104
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105 if (!is.null(chromTIC_merged)) { chromTIC <- chromTIC_merged; chromTIC@phenoData <- xdata@phenoData }
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106 if (!is.null(chromBPI_merged)) { chromBPI <- chromBPI_merged; chromBPI@phenoData <- xdata@phenoData }
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107 if (!is.null(chromTIC_adjusted_merged)) { chromTIC_adjusted <- chromTIC_adjusted_merged; chromTIC_adjusted@phenoData <- xdata@phenoData }
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108 if (!is.null(chromBPI_adjusted_merged)) { chromBPI_adjusted <- chromBPI_adjusted_merged; chromBPI_adjusted@phenoData <- xdata@phenoData }
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109
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110 return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList, "chromTIC"=chromTIC, "chromBPI"=chromBPI, "chromTIC_adjusted"=chromTIC_adjusted, "chromBPI_adjusted"=chromBPI_adjusted))
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111 }
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112
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113 #@author G. Le Corguille
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114 # This function convert if it is required the Retention Time in minutes
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115 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
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116 if (convertRTMinute){
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117 #converting the retention times (seconds) into minutes
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118 print("converting the retention times into minutes in the variableMetadata")
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119 variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60
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120 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60
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121 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60
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122 }
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123 return (variableMetadata)
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124 }
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125
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126 #@author G. Le Corguille
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127 # This function format ions identifiers
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128 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
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129 splitDeco <- strsplit(as.character(variableMetadata$name),"_")
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130 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
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131 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
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132 variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
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133 return(variableMetadata)
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134 }
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135
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136 #@author G. Le Corguille
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137 # Draw the plotChromPeakDensity 3 per page in a pdf file
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138 getPlotChromPeakDensity <- function(xdata, mzdigit=4) {
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139 pdf(file="plotChromPeakDensity.pdf", width=16, height=12)
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140
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141 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
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142
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143 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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144 names(group_colors) <- unique(xdata$sample_group)
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145
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146 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
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147 for (i in 1:nrow(featureDefinitions(xdata))) {
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148 mzmin = featureDefinitions(xdata)[i,]$mzmin
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149 mzmax = featureDefinitions(xdata)[i,]$mzmax
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150 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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151 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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152 }
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153
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154 dev.off()
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155 }
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156
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157 #@author G. Le Corguille
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158 # Draw the plotChromPeakDensity 3 per page in a pdf file
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159 getPlotAdjustedRtime <- function(xdata) {
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160
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161 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
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162
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163 # Color by group
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164 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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165 if (length(group_colors) > 1) {
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166 names(group_colors) <- unique(xdata$sample_group)
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167 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
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168 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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169 }
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170
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171 # Color by sample
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172 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
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173 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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174
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175 dev.off()
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176 }
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177
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178 #@author G. Le Corguille
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179 # value: intensity values to be used into, maxo or intb
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180 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, variableMetadataOutput, dataMatrixOutput) {
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181 dataMatrix <- featureValues(xdata, method="medret", value=intval)
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182 colnames(dataMatrix) <- tools::file_path_sans_ext(colnames(dataMatrix))
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183 dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix)
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184 variableMetadata <- featureDefinitions(xdata)
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185 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
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186 variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata)
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187
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188 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
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189 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
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190
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191 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
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192 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
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193
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194 }
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195
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196 #@author G. Le Corguille
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197 # It allow different of field separators
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198 getDataFrameFromFile <- function(filename, header=T) {
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199 myDataFrame <- read.table(filename, header=header, sep=";", stringsAsFactors=F)
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200 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep="\t", stringsAsFactors=F)
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201 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep=",", stringsAsFactors=F)
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202 if (ncol(myDataFrame) < 2) {
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203 error_message="Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
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204 print(error_message)
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205 stop(error_message)
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206 }
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207 return(myDataFrame)
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208 }
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209
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210 #@author G. Le Corguille
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211 # Draw the BPI and TIC graphics
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212 # colored by sample names or class names
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213 getPlotChromatogram <- function(chrom, xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {
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214
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215 if (aggregationFun == "sum")
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216 type="Total Ion Chromatograms"
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217 else
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218 type="Base Peak Intensity Chromatograms"
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219
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220 adjusted="Raw"
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221 if (hasAdjustedRtime(xdata))
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222 adjusted="Adjusted"
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223
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224 main <- paste(type,":",adjusted,"data")
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225
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226 pdf(pdfname, width=16, height=10)
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227
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228 # Color by group
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229 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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230 if (length(group_colors) > 1) {
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231 names(group_colors) <- unique(xdata$sample_group)
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232 plot(chrom, col = group_colors[chrom$sample_group], main=main)
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233 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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234 }
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235
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236 # Color by sample
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237 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main)
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238 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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239
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240 dev.off()
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241 }
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242
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243
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244 # Get the polarities from all the samples of a condition
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245 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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246 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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247 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
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248 cat("Creating the sampleMetadata file...\n")
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249
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250 #Create the sampleMetada dataframe
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251 sampleMetadata <- xdata@phenoData@data
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252 rownames(sampleMetadata) <- NULL
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253 colnames(sampleMetadata) <- c("sampleMetadata", "class")
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254
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255 sampleNamesOrigin <- sampleMetadata$sampleMetadata
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256 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
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257
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258 if (any(duplicated(sampleNamesMakeNames))) {
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259 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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260 for (sampleName in sampleNamesOrigin) {
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261 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
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262 }
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263 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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264 }
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265
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266 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
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267 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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268 for (sampleName in sampleNamesOrigin) {
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269 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
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270 }
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271 }
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272
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273 sampleMetadata$sampleMetadata <- sampleNamesMakeNames
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274
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275
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276 #For each sample file, the following actions are done
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277 for (fileIdx in 1:length(fileNames(xdata))) {
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278 #Check if the file is in the CDF format
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279 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
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280
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281 # If the column isn't exist, with add one filled with NA
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282 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
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283
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284 #Extract the polarity (a list of polarities)
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285 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
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286 #Verify if all the scans have the same polarity
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287 uniq_list <- unique(polarity)
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288 if (length(uniq_list)>1){
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289 polarity <- "mixed"
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290 } else {
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291 polarity <- as.character(uniq_list)
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292 }
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293
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294 #Set the polarity attribute
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295 sampleMetadata$polarity[fileIdx] <- polarity
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296 }
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297
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298 }
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299
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300 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
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301
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302 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
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303
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304 }
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305
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306
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307 # This function check if xcms will found all the files
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308 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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309 checkFilesCompatibilityWithXcms <- function(directory) {
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310 cat("Checking files filenames compatibilities with xmcs...\n")
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311 # WHAT XCMS WILL FIND
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312 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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313 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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314 info <- file.info(directory)
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315 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
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316 files <- c(directory[!info$isdir], listed)
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317 files_abs <- file.path(getwd(), files)
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318 exists <- file.exists(files_abs)
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319 files[exists] <- files_abs[exists]
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320 files[exists] <- sub("//","/",files[exists])
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321
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322 # WHAT IS ON THE FILESYSTEM
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323 filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T)
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324 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
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325
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326 # COMPARISON
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327 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
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328 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
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329 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
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330 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
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331 }
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332 }
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333
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334
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335 #This function list the compatible files within the directory as xcms did
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336 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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337 getMSFiles <- function (directory) {
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338 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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339 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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340 info <- file.info(directory)
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341 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
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342 files <- c(directory[!info$isdir], listed)
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343 exists <- file.exists(files)
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344 files <- files[exists]
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345 return(files)
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346 }
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347
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348 # This function check if XML contains special caracters. It also checks integrity and completness.
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349 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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350 checkXmlStructure <- function (directory) {
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351 cat("Checking XML structure...\n")
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352
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353 cmd <- paste0("IFS=$'\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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354 capture <- system(cmd, intern=TRUE)
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355
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356 if (length(capture)>0){
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357 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
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358 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
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359 write(capture, stderr())
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360 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
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361 }
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362
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363 }
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364
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365
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366 # This function check if XML contain special characters
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367 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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368 deleteXmlBadCharacters<- function (directory) {
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369 cat("Checking Non ASCII characters in the XML...\n")
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370
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371 processed <- F
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372 l <- system( paste0("find '",directory, "' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"), intern=TRUE)
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373 for (i in l){
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374 cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="")
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375 capture <- suppressWarnings(system(cmd, intern=TRUE))
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376 if (length(capture)>0){
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377 cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
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378 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
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379 c <- system(cmd, intern=TRUE)
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380 capture <- ""
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381 processed <- T
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382 }
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383 }
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384 if (processed) cat("\n\n")
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385 return(processed)
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386 }
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387
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388
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389 # This function will compute MD5 checksum to check the data integrity
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390 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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391 getMd5sum <- function (directory) {
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392 cat("Compute md5 checksum...\n")
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393 # WHAT XCMS WILL FIND
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394 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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395 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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396 info <- file.info(directory)
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397 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
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398 files <- c(directory[!info$isdir], listed)
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399 exists <- file.exists(files)
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400 files <- files[exists]
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401
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402 library(tools)
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403
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404 #cat("\n\n")
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405
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406 return(as.matrix(md5sum(files)))
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407 }
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diff changeset
408
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409
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410 # This function get the raw file path from the arguments
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411 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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412 getRawfilePathFromArguments <- function(singlefile, zipfile, args, prefix="") {
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413 if (!(prefix %in% c("","Positive","Negative","MS1","MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
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414
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415 if (!is.null(args[[paste0("zipfile",prefix)]])) zipfile <- args[[paste0("zipfile",prefix)]]
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416
37
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417 if (!is.null(args[[paste0("singlefile_galaxyPath",prefix)]])) {
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418 singlefile_galaxyPaths <- args[[paste0("singlefile_galaxyPath",prefix)]]
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419 singlefile_sampleNames <- args[[paste0("singlefile_sampleName",prefix)]]
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420 }
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421 if (exists("singlefile_galaxyPaths")){
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422 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\|"))
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423 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\|"))
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424
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425 singlefile <- NULL
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426 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
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427 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
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428 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
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429 # In case, an url is used to import data within Galaxy
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430 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1)
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431 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
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432 }
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433 }
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434 return(list(zipfile=zipfile, singlefile=singlefile))
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435 }
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436
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437 # This function retrieve the raw file in the working directory
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438 # - if zipfile: unzip the file with its directory tree
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439 # - if singlefiles: set symlink with the good filename
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440 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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441 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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442 if(!is.null(singlefile) && (length("singlefile")>0)) {
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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443 for (singlefile_sampleName in names(singlefile)) {
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444 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
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445 if(!file.exists(singlefile_galaxyPath)){
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446 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
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447 print(error_message); stop(error_message)
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lecorguille
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448 }
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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449
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450 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
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451 file.copy(singlefile_galaxyPath, singlefile_sampleName)
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452
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453 }
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454 directory <- "."
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455
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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456 }
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457 if(!is.null(zipfile) && (zipfile != "")) {
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d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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458 if(!file.exists(zipfile)){
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459 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
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d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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diff changeset
460 print(error_message)
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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diff changeset
461 stop(error_message)
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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462 }
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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463
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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464 #list all file in the zip file
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465 #zip_files <- unzip(zipfile,list=T)[,"Name"]
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diff changeset
466
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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diff changeset
467 #unzip
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468 suppressWarnings(unzip(zipfile, unzip="unzip"))
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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parents: 21
diff changeset
469
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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470 #get the directory name
32
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
471 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
472 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
473 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
474 directory <- "."
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
475 if (length(directories) == 1) directory <- directories
24
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
476
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lecorguille
parents: 21
diff changeset
477 cat("files_root_directory\t",directory,"\n")
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
478
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
479 }
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
diff changeset
480 return (directory)
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 21
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481 }
32
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
482
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
483
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
484 # This function retrieve a xset like object
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
485 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
486 getxcmsSetObject <- function(xobject) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
487 # XCMS 1.x
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
488 if (class(xobject) == "xcmsSet")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
489 return (xobject)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
490 # XCMS 3.x
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
491 if (class(xobject) == "XCMSnExp") {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
492 # Get the legacy xcmsSet object
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
493 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
37
9ada611dd63f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
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diff changeset
494 if (!is.null(xset@phenoData$sample_group))
9ada611dd63f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
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diff changeset
495 sampclass(xset) <- xset@phenoData$sample_group
9ada611dd63f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
parents: 36
diff changeset
496 else
9ada611dd63f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
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diff changeset
497 sampclass(xset) <- "."
32
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
498 return (xset)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
499 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
500 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
501
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
502
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
503 #@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
504 # https://github.com/sneumann/xcms/issues/250
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
505 groupnamesW4M <- function(xdata, mzdec = 0, rtdec = 0) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
506 mzfmt <- paste("%.", mzdec, "f", sep = "")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
507 rtfmt <- paste("%.", rtdec, "f", sep = "")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
508
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
509 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
510 sprintf(rtfmt, featureDefinitions(xdata)[,"rtmed"]), sep = "")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
511
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
512 if (any(dup <- duplicated(gnames)))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
513 for (dupname in unique(gnames[dup])) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
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514 dupidx <- which(gnames == dupname)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
515 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
516 }
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lecorguille
parents: 31
diff changeset
517
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
518 return (gnames)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
519 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
520
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
521 #@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
522 # https://github.com/sneumann/xcms/issues/247
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
523 .concatenate_XCMSnExp <- function(...) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
524 x <- list(...)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
525 if (length(x) == 0)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
526 return(NULL)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
527 if (length(x) == 1)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
528 return(x[[1]])
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
529 ## Check that all are XCMSnExp objects.
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
530 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
531 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
532 new_x <- as(.concatenate_OnDiskMSnExp(...), "XCMSnExp")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
533 ## 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
534 ## them!
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
535 x <- lapply(x, function(z) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
536 if (hasAdjustedRtime(z)) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
537 z <- dropAdjustedRtime(z)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
538 warning("Adjusted retention times found, had to drop them.")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
539 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
540 if (hasFeatures(z)) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
541 z <- dropFeatureDefinitions(z)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
542 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
543 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
544 z
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
545 })
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
546 ## Combine peaks
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
547 fls <- lapply(x, fileNames)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
548 startidx <- cumsum(lengths(fls))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
549 pks <- lapply(x, chromPeaks)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
550 procH <- lapply(x, processHistory)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
551 for (i in 2:length(fls)) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
552 pks[[i]][, "sample"] <- pks[[i]][, "sample"] + startidx[i - 1]
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
553 procH[[i]] <- lapply(procH[[i]], function(z) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
554 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
555 z
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
556 })
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
557 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
558 pks <- do.call(rbind, pks)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
559 new_x@.processHistory <- unlist(procH)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
560 chromPeaks(new_x) <- pks
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
561 if (validObject(new_x))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
562 new_x
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
563 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
564
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
565 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
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566 # https://github.com/sneumann/xcms/issues/247
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567 .concatenate_OnDiskMSnExp <- function(...) {
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diff changeset
568 x <- list(...)
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diff changeset
569 if (length(x) == 0)
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570 return(NULL)
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571 if (length(x) == 1)
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572 return(x[[1]])
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573 ## Check that all are XCMSnExp objects.
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574 if (!all(unlist(lapply(x, function(z) is(z, "OnDiskMSnExp")))))
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575 stop("All passed objects should be 'OnDiskMSnExp' objects")
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576 ## Check processingQueue
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577 procQ <- lapply(x, function(z) z@spectraProcessingQueue)
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578 new_procQ <- procQ[[1]]
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579 is_ok <- unlist(lapply(procQ, function(z)
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580 !is.character(all.equal(new_procQ, z))
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lecorguille
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diff changeset
581 ))
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diff changeset
582 if (any(!is_ok)) {
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583 warning("Processing queues from the submitted objects differ! ",
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584 "Dropping the processing queue.")
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diff changeset
585 new_procQ <- list()
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586 }
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587 ## processingData
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588 fls <- lapply(x, function(z) z@processingData@files)
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589 startidx <- cumsum(lengths(fls))
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590 ## featureData
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591 featd <- lapply(x, fData)
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592 ## Have to update the file index and the spectrum names.
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593 for (i in 2:length(featd)) {
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594 featd[[i]]$fileIdx <- featd[[i]]$fileIdx + startidx[i - 1]
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595 rownames(featd[[i]]) <- MSnbase:::formatFileSpectrumNames(
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596 fileIds = featd[[i]]$fileIdx,
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597 spectrumIds = featd[[i]]$spIdx,
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598 nSpectra = nrow(featd[[i]]),
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599 nFiles = length(unlist(fls))
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diff changeset
600 )
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601 }
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602 featd <- do.call(rbind, featd)
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603 featd$spectrum <- 1:nrow(featd)
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604 ## experimentData
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605 expdata <- lapply(x, function(z) {
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606 ed <- z@experimentData
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607 data.frame(instrumentManufacturer = ed@instrumentManufacturer,
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608 instrumentModel = ed@instrumentModel,
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609 ionSource = ed@ionSource,
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610 analyser = ed@analyser,
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611 detectorType = ed@detectorType,
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612 stringsAsFactors = FALSE)
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613 })
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614 expdata <- do.call(rbind, expdata)
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615 expdata <- new("MIAPE",
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616 instrumentManufacturer = expdata$instrumentManufacturer,
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617 instrumentModel = expdata$instrumentModel,
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618 ionSource = expdata$ionSource,
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619 analyser = expdata$analyser,
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620 detectorType = expdata$detectorType)
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621
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622 ## protocolData
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623 protodata <- lapply(x, function(z) z@protocolData)
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624 if (any(unlist(lapply(protodata, nrow)) > 0))
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625 warning("Found non-empty protocol data, but merging protocol data is",
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626 " currently not supported. Skipped.")
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627 ## phenoData
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628 pdata <- do.call(rbind, lapply(x, pData))
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629 res <- new(
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630 "OnDiskMSnExp",
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631 phenoData = new("NAnnotatedDataFrame", data = pdata),
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632 featureData = new("AnnotatedDataFrame", featd),
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633 processingData = new("MSnProcess",
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634 processing = paste0("Concatenated [", date(), "]"),
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635 files = unlist(fls), smoothed = NA),
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636 experimentData = expdata,
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637 spectraProcessingQueue = new_procQ)
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638 if (validObject(res))
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639 res
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640 }
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641
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642 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
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643 # https://github.com/sneumann/xcms/issues/247
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644 c.XCMSnExp <- function(...) {
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645 .concatenate_XCMSnExp(...)
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646 }
35
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diff changeset
647
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648 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
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649 # https://github.com/sneumann/xcms/issues/247
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diff changeset
650 c.MSnbase <- function(...) {
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651 .concatenate_OnDiskMSnExp(...)
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652 }