Mercurial > repos > lecorguille > xcms_merge

annotate lib.r @ 12:9efcd7620cde draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
author lecorguille
date Thu, 05 Apr 2018 18:07:19 -0400
parents 67ab853b89f3
children 40ae497bdc57
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dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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1 #@authors ABiMS TEAM, Y. Guitton
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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3
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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4 #@author G. Le Corguille
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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5 # solve an issue with batch if arguments are logical TRUE/FALSE
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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6 parseCommandArgs <- function(...) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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7 args <- batch::parseCommandArgs(...)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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8 for (key in names(args)) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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9 if (args[key] %in% c("TRUE","FALSE"))
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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10 args[key] = as.logical(args[key])
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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11 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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12 return(args)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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13 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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15 #@author G. Le Corguille
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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16 # This function will
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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17 # - load the packages
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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18 # - display the sessionInfo
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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19 loadAndDisplayPackages <- function(pkgs) {
dca722aecb67 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)))
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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22 sessioninfo = sessionInfo()
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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23 cat(sessioninfo$R.version$version.string,"\n")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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24 cat("Main packages:\n")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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26 cat("Other loaded packages:\n")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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28 }
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30 #@author G. Le Corguille
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31 # This function merge several chromBPI or chromTIC into one.
9efcd7620cde planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
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32 mergeChrom <- function(chromTIC_merged, chromTIC, xdata_merged) {
9efcd7620cde planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
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33 if (is.null(chromTIC_merged)) return(NULL)
9efcd7620cde planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
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34 chromTIC_merged@.Data <- cbind(chromTIC_merged@.Data, chromTIC@.Data)
9efcd7620cde planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
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35 chromTIC_merged@phenoData <- xdata_merged@phenoData
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36 return(chromTIC_merged)
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37 }
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38
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39 #@author G. Le Corguille
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40 # This function merge several xdata into one.
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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41 mergeXData <- function(args) {
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42 chromTIC <- NULL; chromBPI <- NULL
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43 for(image in args$images) {
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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44 load(image)
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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45 # Handle infiles
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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46 if (!exists("singlefile")) singlefile <- NULL
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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47 if (!exists("zipfile")) zipfile <- NULL
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48 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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49 zipfile <- rawFilePath$zipfile
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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50 singlefile <- rawFilePath$singlefile
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51 retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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52 if (exists("raw_data")) xdata <- raw_data
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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53 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
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54 cat(sampleNamesList$sampleNamesOrigin,"\n")
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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55 if (!exists("xdata_merged")) {
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56 xdata_merged <- xdata
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57 singlefile_merged <- singlefile
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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58 md5sumList_merged <- md5sumList
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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59 sampleNamesList_merged <- sampleNamesList
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60 chromTIC_merged <- chromTIC
9efcd7620cde planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
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61 chromBPI_merged <- chromBPI
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62 } else {
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63 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata)
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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64 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata)
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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65 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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66 singlefile_merged <- c(singlefile_merged,singlefile)
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67 md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin)
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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68 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin)
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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69 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames)
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70 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC, xdata_merged)
9efcd7620cde planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
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71 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI, xdata_merged)
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72 }
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73 }
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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74 rm(image)
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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75 xdata <- xdata_merged; rm(xdata_merged)
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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76 singlefile <- singlefile_merged; rm(singlefile_merged)
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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77 md5sumList <- md5sumList_merged; rm(md5sumList_merged)
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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78 sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
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79 chromTIC <- chromTIC_merged; rm(chromTIC_merged)
9efcd7620cde planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
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80 chromBPI <- chromBPI_merged; rm(chromBPI_merged)
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81
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82 if (!is.null(args$sampleMetadata)) {
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83 cat("\tXSET PHENODATA SETTING...\n")
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84 sampleMetadataFile <- args$sampleMetadata
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85 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header=F)
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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86 xdata@phenoData@data$sample_group=sampleMetadata$V2[match(xdata@phenoData@data$sample_name,sampleMetadata$V1)]
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87
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88 if (any(is.na(pData(xdata)$sample_group))) {
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89 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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90 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" "))
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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91 print(error_message)
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92 stop(error_message)
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93 }
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94 }
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95 return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList, "chromTIC"=chromTIC, "chromBPI"=chromBPI))
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96 }
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97
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98 #@author G. Le Corguille
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99 # This function convert if it is required the Retention Time in minutes
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100 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
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101 if (convertRTMinute){
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102 #converting the retention times (seconds) into minutes
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103 print("converting the retention times into minutes in the variableMetadata")
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104 variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60
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105 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60
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106 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60
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107 }
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108 return (variableMetadata)
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109 }
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110
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111 #@author G. Le Corguille
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112 # This function format ions identifiers
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113 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
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114 splitDeco <- strsplit(as.character(variableMetadata$name),"_")
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115 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
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116 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
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117 variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
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118 return(variableMetadata)
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119 }
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120
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121 #@author G. Le Corguille
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122 # Draw the plotChromPeakDensity 3 per page in a pdf file
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123 getPlotChromPeakDensity <- function(xdata, mzdigit=4) {
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124 pdf(file="plotChromPeakDensity.pdf", width=16, height=12)
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125
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126 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
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127
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128 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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129 names(group_colors) <- unique(xdata$sample_group)
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130
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131 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
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132 for (i in 1:nrow(featureDefinitions(xdata))) {
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133 mzmin = featureDefinitions(xdata)[i,]$mzmin
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134 mzmax = featureDefinitions(xdata)[i,]$mzmax
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135 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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136 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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137 }
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138
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139 dev.off()
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140 }
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141
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142 #@author G. Le Corguille
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143 # Draw the plotChromPeakDensity 3 per page in a pdf file
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144 getPlotAdjustedRtime <- function(xdata) {
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145
7
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146 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
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147
7
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148 # Color by group
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149 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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150 if (length(group_colors) > 1) {
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151 names(group_colors) <- unique(xdata$sample_group)
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152 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
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153 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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154 }
10
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155
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156 # Color by sample
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157 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
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158 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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159
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160 dev.off()
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161 }
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162
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163 #@author G. Le Corguille
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164 # value: intensity values to be used into, maxo or intb
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165 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, variableMetadataOutput, dataMatrixOutput) {
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166 dataMatrix <- featureValues(xdata, method="medret", value=intval)
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167 colnames(dataMatrix) <- tools::file_path_sans_ext(colnames(dataMatrix))
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168 dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix)
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169 variableMetadata <- featureDefinitions(xdata)
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170 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
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171 variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata)
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172
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173 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
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174 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
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175
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176 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
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177 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
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178
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179 }
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180
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181 #@author G. Le Corguille
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182 # It allow different of field separators
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183 getDataFrameFromFile <- function(filename, header=T) {
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184 myDataFrame <- read.table(filename, header=header, sep=";", stringsAsFactors=F)
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185 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep="\t", stringsAsFactors=F)
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186 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep=",", stringsAsFactors=F)
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187 if (ncol(myDataFrame) < 2) {
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188 error_message="Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
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189 print(error_message)
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190 stop(error_message)
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191 }
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192 return(myDataFrame)
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193 }
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194
12
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195 getPlotChromatogram <- function(chrom, xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {
10
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196
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197 if (aggregationFun == "sum")
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198 type="Total Ion Chromatograms"
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199 else
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200 type="Base Peak Intensity Chromatograms"
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201
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202 adjusted="Raw"
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203 if (hasAdjustedRtime(xdata))
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204 adjusted="Adjusted"
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205
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206 main <- paste(type,":",adjusted,"data")
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207
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208 pdf(pdfname, width=16, height=10)
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209
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210 # Color by group
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211 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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212 if (length(group_colors) > 1) {
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213 names(group_colors) <- unique(xdata$sample_group)
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214 plot(chrom, col = group_colors[chrom$sample_group], main=main)
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215 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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216 }
10
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217
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218 # Color by sample
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219 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main)
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220 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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221
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222 dev.off()
7
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223 }
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224
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225
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226 # Get the polarities from all the samples of a condition
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227 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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228 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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229 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
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230 cat("Creating the sampleMetadata file...\n")
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231
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232 #Create the sampleMetada dataframe
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233 sampleMetadata <- xdata@phenoData@data
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234 rownames(sampleMetadata) <- NULL
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235 colnames(sampleMetadata) <- c("sampleMetadata", "class")
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236
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237 sampleNamesOrigin <- sampleMetadata$sampleMetadata
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238 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
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239
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240 if (any(duplicated(sampleNamesMakeNames))) {
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241 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())
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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242 for (sampleName in sampleNamesOrigin) {
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243 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
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244 }
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245 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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246 }
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247
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248 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
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249 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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250 for (sampleName in sampleNamesOrigin) {
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251 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
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252 }
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253 }
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254
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255 sampleMetadata$sampleMetadata <- sampleNamesMakeNames
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256
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257
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258 #For each sample file, the following actions are done
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259 for (fileIdx in 1:length(fileNames(xdata))) {
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260 #Check if the file is in the CDF format
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261 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
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262
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263 # If the column isn't exist, with add one filled with NA
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264 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
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265
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266 #Extract the polarity (a list of polarities)
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267 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
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268 #Verify if all the scans have the same polarity
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269 uniq_list <- unique(polarity)
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270 if (length(uniq_list)>1){
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271 polarity <- "mixed"
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272 } else {
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273 polarity <- as.character(uniq_list)
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274 }
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275
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276 #Set the polarity attribute
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277 sampleMetadata$polarity[fileIdx] <- polarity
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278 }
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279
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280 }
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281
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282 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
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283
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284 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
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285
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286 }
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287
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288
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289 # This function check if xcms will found all the files
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290 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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291 checkFilesCompatibilityWithXcms <- function(directory) {
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292 cat("Checking files filenames compatibilities with xmcs...\n")
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293 # WHAT XCMS WILL FIND
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294 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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295 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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296 info <- file.info(directory)
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297 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
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298 files <- c(directory[!info$isdir], listed)
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299 files_abs <- file.path(getwd(), files)
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300 exists <- file.exists(files_abs)
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301 files[exists] <- files_abs[exists]
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302 files[exists] <- sub("//","/",files[exists])
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303
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304 # WHAT IS ON THE FILESYSTEM
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305 filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T)
7
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306 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
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307
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308 # COMPARISON
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309 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
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310 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
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311 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
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312 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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313 }
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314 }
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315
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316
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317 #This function list the compatible files within the directory as xcms did
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318 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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319 getMSFiles <- function (directory) {
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320 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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321 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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322 info <- file.info(directory)
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323 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
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324 files <- c(directory[!info$isdir], listed)
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325 exists <- file.exists(files)
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326 files <- files[exists]
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327 return(files)
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328 }
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329
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330 # This function check if XML contains special caracters. It also checks integrity and completness.
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331 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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332 checkXmlStructure <- function (directory) {
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333 cat("Checking XML structure...\n")
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334
8
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335 cmd <- paste0("IFS=$'\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;")
7
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336 capture <- system(cmd, intern=TRUE)
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337
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338 if (length(capture)>0){
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339 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
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340 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
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341 write(capture, stderr())
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342 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
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343 }
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344
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345 }
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346
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347
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348 # This function check if XML contain special characters
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349 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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350 deleteXmlBadCharacters<- function (directory) {
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351 cat("Checking Non ASCII characters in the XML...\n")
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352
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353 processed <- F
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354 l <- system( paste0("find '",directory, "' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"), intern=TRUE)
7
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355 for (i in l){
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356 cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="")
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357 capture <- suppressWarnings(system(cmd, intern=TRUE))
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358 if (length(capture)>0){
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359 cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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360 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
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361 c <- system(cmd, intern=TRUE)
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362 capture <- ""
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363 processed <- T
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364 }
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365 }
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366 if (processed) cat("\n\n")
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367 return(processed)
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368 }
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369
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370
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
371 # This function will compute MD5 checksum to check the data integrity
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
372 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
373 getMd5sum <- function (directory) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
374 cat("Compute md5 checksum...\n")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
375 # WHAT XCMS WILL FIND
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
376 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
377 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
378 info <- file.info(directory)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
379 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
380 files <- c(directory[!info$isdir], listed)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
381 exists <- file.exists(files)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
382 files <- files[exists]
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
383
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
384 library(tools)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
385
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
386 #cat("\n\n")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
387
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
388 return(as.matrix(md5sum(files)))
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
389 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
390
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
391
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
392 # This function get the raw file path from the arguments
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
393 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
394 getRawfilePathFromArguments <- function(singlefile, zipfile, args) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
395 if (!is.null(args$zipfile)) zipfile <- args$zipfile
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
396 if (!is.null(args$zipfilePositive)) zipfile <- args$zipfilePositive
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
397 if (!is.null(args$zipfileNegative)) zipfile <- args$zipfileNegative
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
398
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
399 if (!is.null(args$singlefile_galaxyPath)) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
400 singlefile_galaxyPaths <- args$singlefile_galaxyPath;
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
401 singlefile_sampleNames <- args$singlefile_sampleName
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
402 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
403 if (!is.null(args$singlefile_galaxyPathPositive)) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
404 singlefile_galaxyPaths <- args$singlefile_galaxyPathPositive;
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
405 singlefile_sampleNames <- args$singlefile_sampleNamePositive
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
406 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
407 if (!is.null(args$singlefile_galaxyPathNegative)) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
408 singlefile_galaxyPaths <- args$singlefile_galaxyPathNegative;
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
409 singlefile_sampleNames <- args$singlefile_sampleNameNegative
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
410 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
411 if (exists("singlefile_galaxyPaths")){
8
6b5504f877ff planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
parents: 7
diff changeset
412 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\|"))
6b5504f877ff planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
parents: 7
diff changeset
413 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\|"))
7
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
414
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
415 singlefile <- NULL
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
416 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
417 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
418 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
419 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
420 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
421 }
11
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 10
diff changeset
422 return(list(zipfile=zipfile, singlefile=singlefile))
7
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
423 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
424
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
425
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
426 # This function retrieve the raw file in the working directory
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
427 # - if zipfile: unzip the file with its directory tree
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
428 # - if singlefiles: set symlink with the good filename
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
429 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
430 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
431 if(!is.null(singlefile) && (length("singlefile")>0)) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
432 for (singlefile_sampleName in names(singlefile)) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
433 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
434 if(!file.exists(singlefile_galaxyPath)){
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
435 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
436 print(error_message); stop(error_message)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
437 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
438
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
439 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
440 file.copy(singlefile_galaxyPath, singlefile_sampleName)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
441
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
442 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
443 directory <- "."
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
444
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
445 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
446 if(!is.null(zipfile) && (zipfile != "")) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
447 if(!file.exists(zipfile)){
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
448 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
449 print(error_message)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
450 stop(error_message)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
451 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
452
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
453 #list all file in the zip file
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
454 #zip_files <- unzip(zipfile,list=T)[,"Name"]
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
455
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
456 #unzip
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
457 suppressWarnings(unzip(zipfile, unzip="unzip"))
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
458
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
459 #get the directory name
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
460 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
461 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
462 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
463 directory <- "."
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
464 if (length(directories) == 1) directory <- directories
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
465
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
466 cat("files_root_directory\t",directory,"\n")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
467
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
468 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
469 return (directory)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
470 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
471
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
472
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
473 # This function retrieve a xset like object
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
474 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
475 getxcmsSetObject <- function(xobject) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
476 # XCMS 1.x
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
477 if (class(xobject) == "xcmsSet")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
478 return (xobject)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
479 # XCMS 3.x
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
480 if (class(xobject) == "XCMSnExp") {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
481 # Get the legacy xcmsSet object
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
482 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
483 sampclass(xset) <- xset@phenoData$sample_group
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
484 return (xset)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
485 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
486 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
487
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
488
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
489 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
490 # https://github.com/sneumann/xcms/issues/250
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
491 groupnamesW4M <- function(xdata, mzdec = 0, rtdec = 0) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
492 mzfmt <- paste("%.", mzdec, "f", sep = "")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
493 rtfmt <- paste("%.", rtdec, "f", sep = "")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
494
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
495 gnames <- paste("M", sprintf(mzfmt, featureDefinitions(xdata)[,"mzmed"]), "T",
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
496 sprintf(rtfmt, featureDefinitions(xdata)[,"rtmed"]), sep = "")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
497
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
498 if (any(dup <- duplicated(gnames)))
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
499 for (dupname in unique(gnames[dup])) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
500 dupidx <- which(gnames == dupname)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
501 gnames[dupidx] <- paste(gnames[dupidx], seq(along = dupidx), sep = "_")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
502 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
503
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
504 return (gnames)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
505 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
506
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
507 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
508 # https://github.com/sneumann/xcms/issues/247
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
509 .concatenate_XCMSnExp <- function(...) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
510 x <- list(...)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
511 if (length(x) == 0)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
512 return(NULL)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
513 if (length(x) == 1)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
514 return(x[[1]])
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
515 ## Check that all are XCMSnExp objects.
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
516 if (!all(unlist(lapply(x, function(z) is(z, "XCMSnExp")))))
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
517 stop("All passed objects should be 'XCMSnExp' objects")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
518 new_x <- as(.concatenate_OnDiskMSnExp(...), "XCMSnExp")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
519 ## If any of the XCMSnExp has alignment results or detected features drop
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
520 ## them!
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
521 x <- lapply(x, function(z) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
522 if (hasAdjustedRtime(z)) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
523 z <- dropAdjustedRtime(z)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
524 warning("Adjusted retention times found, had to drop them.")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
525 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
526 if (hasFeatures(z)) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
527 z <- dropFeatureDefinitions(z)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
528 warning("Feature definitions found, had to drop them.")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
529 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
530 z
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
531 })
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
532 ## Combine peaks
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
533 fls <- lapply(x, fileNames)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
534 startidx <- cumsum(lengths(fls))
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
535 pks <- lapply(x, chromPeaks)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
536 procH <- lapply(x, processHistory)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
537 for (i in 2:length(fls)) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
538 pks[[i]][, "sample"] <- pks[[i]][, "sample"] + startidx[i - 1]
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
539 procH[[i]] <- lapply(procH[[i]], function(z) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
540 z@fileIndex <- as.integer(z@fileIndex + startidx[i - 1])
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
541 z
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
542 })
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
543 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
544 pks <- do.call(rbind, pks)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
545 new_x@.processHistory <- unlist(procH)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
546 chromPeaks(new_x) <- pks
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
547 if (validObject(new_x))
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
548 new_x
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
549 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
550
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
551 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
552 # https://github.com/sneumann/xcms/issues/247
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
553 .concatenate_OnDiskMSnExp <- function(...) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
554 x <- list(...)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
555 if (length(x) == 0)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
556 return(NULL)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
557 if (length(x) == 1)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
558 return(x[[1]])
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
559 ## Check that all are XCMSnExp objects.
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
560 if (!all(unlist(lapply(x, function(z) is(z, "OnDiskMSnExp")))))
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
561 stop("All passed objects should be 'OnDiskMSnExp' objects")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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parents:
diff changeset
562 ## Check processingQueue
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
563 procQ <- lapply(x, function(z) z@spectraProcessingQueue)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
564 new_procQ <- procQ[[1]]
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
565 is_ok <- unlist(lapply(procQ, function(z)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
566 !is.character(all.equal(new_procQ, z))
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
567 ))
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
568 if (any(!is_ok)) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
569 warning("Processing queues from the submitted objects differ! ",
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
570 "Dropping the processing queue.")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
571 new_procQ <- list()
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
572 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
573 ## processingData
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
574 fls <- lapply(x, function(z) z@processingData@files)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
575 startidx <- cumsum(lengths(fls))
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
576 ## featureData
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
577 featd <- lapply(x, fData)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
578 ## Have to update the file index and the spectrum names.
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
579 for (i in 2:length(featd)) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
580 featd[[i]]$fileIdx <- featd[[i]]$fileIdx + startidx[i - 1]
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
581 rownames(featd[[i]]) <- MSnbase:::formatFileSpectrumNames(
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
582 fileIds = featd[[i]]$fileIdx,
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
583 spectrumIds = featd[[i]]$spIdx,
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
584 nSpectra = nrow(featd[[i]]),
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
585 nFiles = length(unlist(fls))
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
586 )
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
587 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
588 featd <- do.call(rbind, featd)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
589 featd$spectrum <- 1:nrow(featd)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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590 ## experimentData
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
591 expdata <- lapply(x, function(z) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
592 ed <- z@experimentData
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
593 data.frame(instrumentManufacturer = ed@instrumentManufacturer,
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
594 instrumentModel = ed@instrumentModel,
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
595 ionSource = ed@ionSource,
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
596 analyser = ed@analyser,
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
597 detectorType = ed@detectorType,
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
598 stringsAsFactors = FALSE)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
599 })
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
600 expdata <- do.call(rbind, expdata)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
601 expdata <- new("MIAPE",
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
602 instrumentManufacturer = expdata$instrumentManufacturer,
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
603 instrumentModel = expdata$instrumentModel,
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
604 ionSource = expdata$ionSource,
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
605 analyser = expdata$analyser,
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
606 detectorType = expdata$detectorType)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
607
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
608 ## protocolData
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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609 protodata <- lapply(x, function(z) z@protocolData)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
610 if (any(unlist(lapply(protodata, nrow)) > 0))
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
611 warning("Found non-empty protocol data, but merging protocol data is",
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
612 " currently not supported. Skipped.")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
613 ## phenoData
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
614 pdata <- do.call(rbind, lapply(x, pData))
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
615 res <- new(
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
616 "OnDiskMSnExp",
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
617 phenoData = new("NAnnotatedDataFrame", data = pdata),
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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618 featureData = new("AnnotatedDataFrame", featd),
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
619 processingData = new("MSnProcess",
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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620 processing = paste0("Concatenated [", date(), "]"),
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
621 files = unlist(fls), smoothed = NA),
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
622 experimentData = expdata,
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
623 spectraProcessingQueue = new_procQ)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
624 if (validObject(res))
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
625 res
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
626 }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
627
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
628 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
629 # https://github.com/sneumann/xcms/issues/247
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
630 c.XCMSnExp <- function(...) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
631 .concatenate_XCMSnExp(...)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
632 }
11
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 10
diff changeset
633
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 10
diff changeset
634 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 10
diff changeset
635 # https://github.com/sneumann/xcms/issues/247
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 10
diff changeset
636 c.MSnbase <- function(...) {
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 10
diff changeset
637 .concatenate_OnDiskMSnExp(...)
67ab853b89f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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diff changeset
638 }