Mercurial > repos > lecorguille > xcms_xcmsset

annotate xcms_xcmsSet.r @ 23:5c62dfdb64f4 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4632d03b53c344757d71dd3310d37069fb498b26
author lecorguille
date Tue, 12 Mar 2019 10:59:28 -0400
parents 87df3692c68d
children 9a0ca3f3a847
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1 #!/usr/bin/env Rscript
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3 # ----- LOG FILE -----
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4 log_file <- file("log.txt", open="wt")
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5 sink(log_file)
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6 sink(log_file, type = "output")
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9 # ----- PACKAGE -----
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10 cat("\tSESSION INFO\n")
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12 #Import the different functions
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13 source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
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14 source_local("lib.r")
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16 pkgs <- c("xcms","batch")
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17 loadAndDisplayPackages(pkgs)
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18 cat("\n\n");
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21 # ----- ARGUMENTS -----
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22 cat("\tARGUMENTS INFO\n")
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23 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects
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24 write.table(as.matrix(args), col.names=F, quote=F, sep='\t')
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26 cat("\n\n")
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29 # ----- PROCESSING INFILE -----
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30 cat("\tARGUMENTS PROCESSING INFO\n")
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32 #saving the commun parameters
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33 BPPARAM <- MulticoreParam(1)
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34 if (!is.null(args$BPPARAM)){
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35 BPPARAM <- MulticoreParam(args$BPPARAM)
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36 }
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37 register(BPPARAM)
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39 #saving the specific parameters
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40 if (!is.null(args$filterAcquisitionNum)) filterAcquisitionNumParam <- args$filterAcquisitionNum
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41 if (!is.null(args$filterRt)) filterRtParam <- args$filterRt
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42 if (!is.null(args$filterMz)) filterMzParam <- args$filterMz
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44 method <- args$method
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46 if (!is.null(args$roiList)){
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47 cat("\t\troiList provided\n")
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48 args$roiList <- list(getDataFrameFromFile(args$roiList))
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49 print(args$roiList)
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50 }
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52 cat("\n\n")
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54 # ----- INFILE PROCESSING -----
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55 cat("\tINFILE PROCESSING INFO\n")
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57 #image is an .RData file necessary to use xset variable given by previous tools
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58 load(args$image)
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59 if (!exists("raw_data")) stop("\n\nERROR: The RData doesn't contain any object called 'raw_data' which is provided by the tool: MSnbase readMSData")
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61 # Handle infiles
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62 if (!exists("singlefile")) singlefile <- NULL
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63 if (!exists("zipfile")) zipfile <- NULL
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64 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
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65 zipfile <- rawFilePath$zipfile
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66 singlefile <- rawFilePath$singlefile
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67 directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
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70 cat("\n\n")
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73 # ----- MAIN PROCESSING INFO -----
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74 cat("\tMAIN PROCESSING INFO\n")
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77 cat("\t\tCOMPUTE\n")
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79 ## Get the full path to the files
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80 files <- getMSFiles(directory)
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82 cat("\t\t\tApply filter[s] (if asked)\n")
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83 if (exists("filterAcquisitionNumParam")) raw_data <- filterAcquisitionNum(raw_data, filterAcquisitionNumParam[1]:filterAcquisitionNumParam[2])
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84 if (exists("filterRtParam")) raw_data <- filterRt(raw_data, filterRtParam)
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85 if (exists("filterMzParam")) raw_data <- filterMz(raw_data, filterMzParam)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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86 #Apply this filter only if file contain MS and MSn
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87 if(length(unique(msLevel(raw_data)))!= 1){
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88 raw_data <- filterMsLevel(raw_data,msLevel=1)
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89 }
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91 cat("\t\t\tChromatographic peak detection\n")
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92 # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ...
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93 args <- args[names(args) %in% slotNames(do.call(paste0(method,"Param"), list()))]
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95 findChromPeaksParam <- do.call(paste0(method,"Param"), args)
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96 print(findChromPeaksParam)
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97 xdata <- findChromPeaks(raw_data, param=findChromPeaksParam)
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98
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99 # Check if there are no peaks
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100 if (nrow(chromPeaks(xdata)) == 0) stop("No peaks were detected. You should review your settings")
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101
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102 # Transform the files absolute pathways into relative pathways
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103 xdata@processingData@files <- sub(paste(getwd(), "/", sep="") , "", xdata@processingData@files)
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104
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105 # Create a sampleMetada file
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106 sampleNamesList <- getSampleMetadata(xdata=xdata, sampleMetadataOutput="sampleMetadata.tsv")
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107
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108 cat("\t\t\tCompute and Store TIC and BPI\n")
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109 chromTIC = chromatogram(xdata, aggregationFun = "sum")
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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110 chromBPI = chromatogram(xdata, aggregationFun = "max")
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111
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112 cat("\n\n")
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113
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114 # ----- EXPORT -----
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115
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116 cat("\tXCMSnExp OBJECT INFO\n")
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117 print(xdata)
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118 cat("\n\n")
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119
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120 cat("\txcmsSet OBJECT INFO\n")
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121 # Get the legacy xcmsSet object
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122 xset <- getxcmsSetObject(xdata)
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123 print(xset)
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124 cat("\n\n")
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125
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126 #saving R data in .Rdata file to save the variables used in the present tool
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127 objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList", "chromTIC", "chromBPI")
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128 save(list=objects2save[objects2save %in% ls()], file="xcmsSet.RData")
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129
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130
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131 cat("\tDONE\n")