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annotate lib.r @ 25:a066b8581b97 draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 42a0bcde81726702194f1b4ecd741d0545648d40"
author workflow4metabolomics
date Tue, 28 Apr 2020 09:34:27 -0400
parents 761913919c21
children 0d05d0458376
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833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
1 #@authors ABiMS TEAM, Y. Guitton
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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3
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
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4 #@author G. Le Corguille
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
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5 # solve an issue with batch if arguments are logical TRUE/FALSE
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
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6 parseCommandArgs <- function(...) {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
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7 args <- batch::parseCommandArgs(...)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
8 for (key in names(args)) {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
9 if (args[key] %in% c("TRUE","FALSE"))
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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10 args[key] = as.logical(args[key])
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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11 }
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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12 return(args)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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13 }
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2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
15 #@author G. Le Corguille
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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16 # This function will
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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17 # - load the packages
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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18 # - display the sessionInfo
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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19 loadAndDisplayPackages <- function(pkgs) {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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20 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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22 sessioninfo = sessionInfo()
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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23 cat(sessioninfo$R.version$version.string,"\n")
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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24 cat("Main packages:\n")
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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26 cat("Other loaded packages:\n")
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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28 }
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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30 #@author G. Le Corguille
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
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31 # This function merge several chromBPI or chromTIC into one.
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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32 mergeChrom <- function(chrom_merged, chrom) {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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33 if (is.null(chrom_merged)) return(NULL)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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34 chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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35 return(chrom_merged)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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36 }
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lecorguille
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38 #@author G. Le Corguille
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lecorguille
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39 # This function merge several xdata into one.
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
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40 mergeXData <- function(args) {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
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41 chromTIC <- NULL
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
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42 chromBPI <- NULL
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
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43 chromTIC_adjusted <- NULL
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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44 chromBPI_adjusted <- NULL
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761913919c21 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
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45 md5sumList <- NULL
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lecorguille
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46 for(image in args$images) {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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48 load(image)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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49 # Handle infiles
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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50 if (!exists("singlefile")) singlefile <- NULL
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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51 if (!exists("zipfile")) zipfile <- NULL
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761913919c21 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
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52 rawFilePath <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile, args)
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833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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53 zipfile <- rawFilePath$zipfile
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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54 singlefile <- rawFilePath$singlefile
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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lecorguille
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56 if (exists("raw_data")) xdata <- raw_data
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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57 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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lecorguille
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59 cat(sampleNamesList$sampleNamesOrigin,"\n")
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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61 if (!exists("xdata_merged")) {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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62 xdata_merged <- xdata
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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63 singlefile_merged <- singlefile
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
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64 md5sumList_merged <- md5sumList
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
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65 sampleNamesList_merged <- sampleNamesList
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
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66 chromTIC_merged <- chromTIC
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
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67 chromBPI_merged <- chromBPI
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
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68 chromTIC_adjusted_merged <- chromTIC_adjusted
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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69 chromBPI_adjusted_merged <- chromBPI_adjusted
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
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70 } else {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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71 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata)
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lecorguille
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72 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged,xdata)
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833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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73 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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lecorguille
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75 singlefile_merged <- c(singlefile_merged,singlefile)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
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76 md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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77 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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78 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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79 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
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80 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
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81 chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
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82 chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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83 }
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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84 }
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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85 rm(image)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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86 xdata <- xdata_merged; rm(xdata_merged)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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87 singlefile <- singlefile_merged; rm(singlefile_merged)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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88 md5sumList <- md5sumList_merged; rm(md5sumList_merged)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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89 sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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90
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91 if (!is.null(args$sampleMetadata)) {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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92 cat("\tXSET PHENODATA SETTING...\n")
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93 sampleMetadataFile <- args$sampleMetadata
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94 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header=F)
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95 xdata@phenoData@data$sample_group=sampleMetadata$V2[match(xdata@phenoData@data$sample_name,sampleMetadata$V1)]
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96
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97 if (any(is.na(pData(xdata)$sample_group))) {
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98 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
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99 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" "))
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100 print(error_message)
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101 stop(error_message)
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102 }
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103 }
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104
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105 if (!is.null(chromTIC_merged)) { chromTIC <- chromTIC_merged; chromTIC@phenoData <- xdata@phenoData }
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106 if (!is.null(chromBPI_merged)) { chromBPI <- chromBPI_merged; chromBPI@phenoData <- xdata@phenoData }
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107 if (!is.null(chromTIC_adjusted_merged)) { chromTIC_adjusted <- chromTIC_adjusted_merged; chromTIC_adjusted@phenoData <- xdata@phenoData }
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108 if (!is.null(chromBPI_adjusted_merged)) { chromBPI_adjusted <- chromBPI_adjusted_merged; chromBPI_adjusted@phenoData <- xdata@phenoData }
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109
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110 return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList, "chromTIC"=chromTIC, "chromBPI"=chromBPI, "chromTIC_adjusted"=chromTIC_adjusted, "chromBPI_adjusted"=chromBPI_adjusted))
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111 }
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112
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113 #@author G. Le Corguille
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114 # This function convert if it is required the Retention Time in minutes
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115 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
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116 if (convertRTMinute){
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117 #converting the retention times (seconds) into minutes
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118 print("converting the retention times into minutes in the variableMetadata")
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119 variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60
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120 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60
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121 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60
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122 }
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123 return (variableMetadata)
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124 }
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125
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126 #@author G. Le Corguille
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127 # This function format ions identifiers
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128 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
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129 splitDeco <- strsplit(as.character(variableMetadata$name),"_")
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130 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
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131 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
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132 variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
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133 return(variableMetadata)
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134 }
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135
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136 #@author G. Le Corguille
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137 # This function convert the remain NA to 0 in the dataMatrix
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138 naTOzeroDataMatrix <- function(dataMatrix, naTOzero) {
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139 if (naTOzero){
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140 dataMatrix[is.na(dataMatrix)] <- 0
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141 }
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142 return (dataMatrix)
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143 }
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144
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145 #@author G. Le Corguille
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146 # Draw the plotChromPeakDensity 3 per page in a pdf file
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147 getPlotChromPeakDensity <- function(xdata, param = NULL, mzdigit=4) {
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148 pdf(file="plotChromPeakDensity.pdf", width=16, height=12)
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149
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150 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
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151
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152 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
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153 names(group_colors) <- unique(xdata$sample_group)
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154 col_per_samp <- as.character(xdata$sample_group)
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155 for(i in 1:length(group_colors)){col_per_samp[col_per_samp==(names(group_colors)[i])]<-group_colors[i]}
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156
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157 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
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158 for (i in 1:nrow(featureDefinitions(xdata))) {
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159 mzmin = featureDefinitions(xdata)[i,]$mzmin
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160 mzmax = featureDefinitions(xdata)[i,]$mzmax
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161 plotChromPeakDensity(xdata, param = param, mz=c(mzmin,mzmax), col=col_per_samp, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
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162 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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163 }
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164
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165 dev.off()
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166 }
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167
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168 #@author G. Le Corguille
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169 # Draw the plotChromPeakDensity 3 per page in a pdf file
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170 getPlotAdjustedRtime <- function(xdata) {
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171
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172 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
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173
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174 # Color by group
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175 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
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176 if (length(group_colors) > 1) {
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177 names(group_colors) <- unique(xdata$sample_group)
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178 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
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179 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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180 }
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181
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182 # Color by sample
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183 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
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184 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)
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185
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186 dev.off()
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187 }
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188
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189 #@author G. Le Corguille
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190 # value: intensity values to be used into, maxo or intb
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191 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, naTOzero=T, variableMetadataOutput, dataMatrixOutput, sampleNamesList) {
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192 dataMatrix <- featureValues(xdata, method="medret", value=intval)
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193 colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix)))
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194 dataMatrix = cbind(name=groupnames(xdata), dataMatrix)
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195 variableMetadata <- featureDefinitions(xdata)
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196 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
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197 variableMetadata = data.frame(name=groupnames(xdata), variableMetadata)
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198
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199 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
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200 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
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201 dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)
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202
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203 # FIX: issue when the vector at peakidx is too long and is written in a new line during the export
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204 variableMetadata[,"peakidx"] <- vapply(variableMetadata[,"peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",")
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205
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206 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
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207 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
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208
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209 }
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210
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211 #@author G. Le Corguille
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212 # It allow different of field separators
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213 getDataFrameFromFile <- function(filename, header=T) {
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214 myDataFrame <- read.table(filename, header=header, sep=";", stringsAsFactors=F)
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215 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep="\t", stringsAsFactors=F)
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216 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep=",", stringsAsFactors=F)
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217 if (ncol(myDataFrame) < 2) {
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218 error_message="Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
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219 print(error_message)
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220 stop(error_message)
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221 }
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222 return(myDataFrame)
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223 }
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224
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225 #@author G. Le Corguille
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226 # Draw the BPI and TIC graphics
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227 # colored by sample names or class names
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228 getPlotChromatogram <- function(chrom, xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {
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229
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230 if (aggregationFun == "sum")
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231 type="Total Ion Chromatograms"
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232 else
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233 type="Base Peak Intensity Chromatograms"
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234
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235 adjusted="Raw"
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236 if (hasAdjustedRtime(xdata))
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237 adjusted="Adjusted"
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238
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239 main <- paste(type,":",adjusted,"data")
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240
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241 pdf(pdfname, width=16, height=10)
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242
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243 # Color by group
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244 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
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245 if (length(group_colors) > 1) {
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246 names(group_colors) <- unique(xdata$sample_group)
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247 plot(chrom, col = group_colors[as.factor(chrom$sample_group)], main=main, peakType = "none")
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248 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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249 }
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250
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251 # Color by sample
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252 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main, peakType = "none")
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253 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)
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254
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255 dev.off()
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256 }
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257
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258
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259 # Get the polarities from all the samples of a condition
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260 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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261 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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262 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
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263 cat("Creating the sampleMetadata file...\n")
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264
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265 #Create the sampleMetada dataframe
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266 sampleMetadata <- xdata@phenoData@data
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267 rownames(sampleMetadata) <- NULL
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268 colnames(sampleMetadata) <- c("sample_name", "class")
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269
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270 sampleNamesOrigin <- sampleMetadata$sample_name
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271 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
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272
10
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273 if (any(duplicated(sampleNamesMakeNames))) {
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274 write("\n\nERROR: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names().\nIn your case, at least two columns after the renaming obtain the same name, thus XCMS will collapse those columns per name.", stderr())
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275 for (sampleName in sampleNamesOrigin) {
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276 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
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277 }
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278 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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279 }
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280
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281 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
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282 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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283 for (sampleName in sampleNamesOrigin) {
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284 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
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285 }
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286 }
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287
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288 sampleMetadata$sample_name <- sampleNamesMakeNames
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289
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290
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291 #For each sample file, the following actions are done
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292 for (fileIdx in 1:length(fileNames(xdata))) {
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293 #Check if the file is in the CDF format
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294 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
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295
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296 # If the column isn't exist, with add one filled with NA
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297 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
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298
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299 #Extract the polarity (a list of polarities)
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300 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
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301 #Verify if all the scans have the same polarity
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302 uniq_list <- unique(polarity)
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303 if (length(uniq_list)>1){
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304 polarity <- "mixed"
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305 } else {
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306 polarity <- as.character(uniq_list)
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307 }
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308
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309 #Set the polarity attribute
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310 sampleMetadata$polarity[fileIdx] <- polarity
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311 }
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312
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313 }
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314
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315 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
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316
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317 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
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318
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319 }
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320
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321
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322 # This function will compute MD5 checksum to check the data integrity
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323 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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324 getMd5sum <- function (files) {
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325 cat("Compute md5 checksum...\n")
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326 library(tools)
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327 return(as.matrix(md5sum(files)))
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328 }
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329
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330 # This function retrieve the raw file in the working directory
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331 # - if zipfile: unzip the file with its directory tree
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332 # - if singlefiles: set symlink with the good filename
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333 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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334 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile, args, prefix="") {
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335
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336 if (!(prefix %in% c("","Positive","Negative","MS1","MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
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337
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338 # single - if the file are passed in the command arguments -> refresh singlefile
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339 if (!is.null(args[[paste0("singlefile_galaxyPath",prefix)]])) {
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340 singlefile_galaxyPaths <- unlist(strsplit(args[[paste0("singlefile_galaxyPath",prefix)]],"\\|"))
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341 singlefile_sampleNames <- unlist(strsplit(args[[paste0("singlefile_sampleName",prefix)]],"\\|"))
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342
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343 singlefile <- NULL
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344 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
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345 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
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346 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
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347 # In case, an url is used to import data within Galaxy
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348 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1)
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349 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
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350 }
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351 }
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352 # zipfile - if the file are passed in the command arguments -> refresh zipfile
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353 if (!is.null(args[[paste0("zipfile",prefix)]]))
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354 zipfile <- args[[paste0("zipfile",prefix)]]
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355
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356 # single
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357 if(!is.null(singlefile) && (length("singlefile")>0)) {
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358 files <- vector()
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359 for (singlefile_sampleName in names(singlefile)) {
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360 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
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361 if(!file.exists(singlefile_galaxyPath)){
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362 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
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363 print(error_message); stop(error_message)
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364 }
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365
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366 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
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367 file.copy(singlefile_galaxyPath, singlefile_sampleName)
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368 files <- c(files, singlefile_sampleName)
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369 }
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370 }
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371 # zipfile
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372 if(!is.null(zipfile) && (zipfile != "")) {
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373 if(!file.exists(zipfile)){
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374 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
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375 print(error_message)
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376 stop(error_message)
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377 }
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378 suppressWarnings(unzip(zipfile, unzip="unzip"))
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379
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380 #get the directory name
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381 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
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382 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))
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383 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
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384 directory <- "."
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385 if (length(directories) == 1) directory <- directories
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386
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387 cat("files_root_directory\t",directory,"\n")
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388
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389 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
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390 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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391 info <- file.info(directory)
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392 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
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393 files <- c(directory[!info$isdir], listed)
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394 exists <- file.exists(files)
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395 files <- files[exists]
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396
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397 }
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398 return(list(zipfile=zipfile, singlefile=singlefile, files=files))
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399
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400 }
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401
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402
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403 # This function retrieve a xset like object
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404 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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405 getxcmsSetObject <- function(xobject) {
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406 # XCMS 1.x
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407 if (class(xobject) == "xcmsSet")
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408 return (xobject)
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409 # XCMS 3.x
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410 if (class(xobject) == "XCMSnExp") {
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411 # Get the legacy xcmsSet object
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412 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
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413 if (!is.null(xset@phenoData$sample_group))
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414 sampclass(xset) <- xset@phenoData$sample_group
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415 else
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416 sampclass(xset) <- "."
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417 return (xset)
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418 }
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419 }