Mercurial > repos > lecorguille > xcms_retcor

annotate xcms_retcor.r @ 30:4d6f4cd7c3ef draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
author lecorguille
date Thu, 01 Mar 2018 04:16:45 -0500
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children 1aa7979204b4
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30
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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1 #!/usr/bin/env Rscript
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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lecorguille
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3 # ----- LOG FILE -----
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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4 log_file=file("log.txt", open = "wt")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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5 sink(log_file)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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6 sink(log_file, type = "output")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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9 # ----- PACKAGE -----
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10 cat("\tSESSION INFO\n")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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12 #Import the different functions
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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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="/")) }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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14 source_local("lib.r")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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16 pkgs <- c("xcms","batch","RColorBrewer")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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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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28 # ----- PROCESSING INFILE -----
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29 cat("\tARGUMENTS PROCESSING INFO\n")
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31 #saving the specific parameters
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32 method <- args$method; args$method <- NULL
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34 cat("\n\n")
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37 # ----- ARGUMENTS PROCESSING -----
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38 cat("\tINFILE PROCESSING INFO\n")
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39
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40 #image is an .RData file necessary to use xset variable given by previous tools
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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41 load(args$image); args$image=NULL
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42 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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44 # Handle infiles
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45 if (!exists("singlefile")) singlefile <- NULL
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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46 if (!exists("zipfile")) zipfile <- NULL
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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47 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
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48 zipfile <- rawFilePath$zipfile
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49 singlefile <- rawFilePath$singlefile
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50 args <- rawFilePath$args
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51 directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
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53 # Check some character issues
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54 md5sumList <- list("origin" = getMd5sum(directory))
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55 checkXmlStructure(directory)
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56 checkFilesCompatibilityWithXcms(directory)
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59 cat("\n\n")
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62 # ----- MAIN PROCESSING INFO -----
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63 cat("\tMAIN PROCESSING INFO\n")
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66 cat("\t\tCOMPUTE\n")
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68 cat("\t\t\tAlignment/Retention Time correction\n")
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69 adjustRtimeParam <- do.call(paste0(method,"Param"), args)
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70 print(adjustRtimeParam)
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71 xdata <- adjustRtime(xdata, param=adjustRtimeParam)
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73 # Get the legacy xcmsSet object
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74 xset <- getxcmsSetObject(xdata)
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76 cat("\n\n")
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79 # -- TIC --
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80 cat("\t\tDRAW GRAPHICS\n")
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81 getPlotAdjustedRtime(xdata)
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83 #@TODO: one day, use xdata instead of xset to draw the TICs and BPC or a complete other method
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84 getTICs(xcmsSet=xset, rt="raw", pdfname="TICs.pdf")
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85 getBPCs(xcmsSet=xset, rt="raw", pdfname="BICs.pdf")
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87 cat("\n\n")
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89 # ----- EXPORT -----
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91 cat("\tXCMSnExp OBJECT INFO\n")
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92 print(xdata)
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93 cat("\n\n")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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94
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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95 cat("\txcmsSet OBJECT INFO\n")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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96 print(xset)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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97 cat("\n\n")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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98
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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99 #saving R data in .Rdata file to save the variables used in the present tool
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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100 objects2save = c("xdata","zipfile","singlefile","md5sumList","sampleNamesList")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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101 save(list=objects2save[objects2save %in% ls()], file="retcor.RData")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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102
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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103 cat("\n\n")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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104
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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105
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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106 cat("\tDONE\n")