Mercurial > repos > lecorguille > xcms_summary
annotate lib.r @ 25:acc66e5c23d7 draft
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
author | workflow4metabolomics |
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date | Wed, 12 Feb 2020 08:30:41 -0500 |
parents | acc0a4a366c1 |
children | db6549f27ad1 |
rev | line source |
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97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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1 #@authors ABiMS TEAM, Y. Guitton |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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2 # lib.r for Galaxy Workflow4Metabolomics xcms tools |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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3 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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4 #@author G. Le Corguille |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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5 # solve an issue with batch if arguments are logical TRUE/FALSE |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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6 parseCommandArgs <- function(...) { |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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7 args <- batch::parseCommandArgs(...) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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8 for (key in names(args)) { |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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9 if (args[key] %in% c("TRUE","FALSE")) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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10 args[key] = as.logical(args[key]) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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11 } |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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12 return(args) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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13 } |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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14 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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15 #@author G. Le Corguille |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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16 # This function will |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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17 # - load the packages |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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18 # - display the sessionInfo |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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19 loadAndDisplayPackages <- function(pkgs) { |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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20 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE))) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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21 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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22 sessioninfo = sessionInfo() |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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23 cat(sessioninfo$R.version$version.string,"\n") |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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24 cat("Main packages:\n") |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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26 cat("Other loaded packages:\n") |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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28 } |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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29 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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30 #@author G. Le Corguille |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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31 # This function merge several chromBPI or chromTIC into one. |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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32 mergeChrom <- function(chrom_merged, chrom) { |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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33 if (is.null(chrom_merged)) return(NULL) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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34 chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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35 return(chrom_merged) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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36 } |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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37 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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38 #@author G. Le Corguille |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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39 # This function merge several xdata into one. |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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40 mergeXData <- function(args) { |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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41 chromTIC <- NULL |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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42 chromBPI <- NULL |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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43 chromTIC_adjusted <- NULL |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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44 chromBPI_adjusted <- NULL |
25
acc66e5c23d7
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents:
24
diff
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45 md5sumList <- NULL |
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97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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46 for(image in args$images) { |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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47 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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48 load(image) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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49 # Handle infiles |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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50 if (!exists("singlefile")) singlefile <- NULL |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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51 if (!exists("zipfile")) zipfile <- NULL |
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acc66e5c23d7
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
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52 rawFilePath <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile, args) |
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97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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53 zipfile <- rawFilePath$zipfile |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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54 singlefile <- rawFilePath$singlefile |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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55 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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56 if (exists("raw_data")) xdata <- raw_data |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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57 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*") |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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58 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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59 cat(sampleNamesList$sampleNamesOrigin,"\n") |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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60 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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61 if (!exists("xdata_merged")) { |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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62 xdata_merged <- xdata |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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63 singlefile_merged <- singlefile |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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64 md5sumList_merged <- md5sumList |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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65 sampleNamesList_merged <- sampleNamesList |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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66 chromTIC_merged <- chromTIC |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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67 chromBPI_merged <- chromBPI |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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68 chromTIC_adjusted_merged <- chromTIC_adjusted |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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69 chromBPI_adjusted_merged <- chromBPI_adjusted |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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70 } else { |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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71 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata) |
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7941015d6fc0
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4632d03b53c344757d71dd3310d37069fb498b26
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72 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged,xdata) |
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97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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73 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata") |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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74 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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75 singlefile_merged <- c(singlefile_merged,singlefile) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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76 md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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77 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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78 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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79 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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80 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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81 chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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82 chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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83 } |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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84 } |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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85 rm(image) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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86 xdata <- xdata_merged; rm(xdata_merged) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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87 singlefile <- singlefile_merged; rm(singlefile_merged) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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88 md5sumList <- md5sumList_merged; rm(md5sumList_merged) |
97ca0321931b
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89 sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged) |
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90 |
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91 if (!is.null(args$sampleMetadata)) { |
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92 cat("\tXSET PHENODATA SETTING...\n") |
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93 sampleMetadataFile <- args$sampleMetadata |
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94 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header=F) |
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95 xdata@phenoData@data$sample_group=sampleMetadata$V2[match(xdata@phenoData@data$sample_name,sampleMetadata$V1)] |
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96 |
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97 if (any(is.na(pData(xdata)$sample_group))) { |
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98 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)] |
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99 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" ")) |
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100 print(error_message) |
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101 stop(error_message) |
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102 } |
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103 } |
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104 |
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105 if (!is.null(chromTIC_merged)) { chromTIC <- chromTIC_merged; chromTIC@phenoData <- xdata@phenoData } |
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106 if (!is.null(chromBPI_merged)) { chromBPI <- chromBPI_merged; chromBPI@phenoData <- xdata@phenoData } |
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107 if (!is.null(chromTIC_adjusted_merged)) { chromTIC_adjusted <- chromTIC_adjusted_merged; chromTIC_adjusted@phenoData <- xdata@phenoData } |
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108 if (!is.null(chromBPI_adjusted_merged)) { chromBPI_adjusted <- chromBPI_adjusted_merged; chromBPI_adjusted@phenoData <- xdata@phenoData } |
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109 |
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110 return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList, "chromTIC"=chromTIC, "chromBPI"=chromBPI, "chromTIC_adjusted"=chromTIC_adjusted, "chromBPI_adjusted"=chromBPI_adjusted)) |
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111 } |
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112 |
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113 #@author G. Le Corguille |
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114 # This function convert if it is required the Retention Time in minutes |
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115 RTSecondToMinute <- function(variableMetadata, convertRTMinute) { |
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116 if (convertRTMinute){ |
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117 #converting the retention times (seconds) into minutes |
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118 print("converting the retention times into minutes in the variableMetadata") |
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119 variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60 |
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120 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60 |
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121 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60 |
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122 } |
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123 return (variableMetadata) |
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124 } |
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125 |
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126 #@author G. Le Corguille |
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127 # This function format ions identifiers |
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128 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) { |
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129 splitDeco <- strsplit(as.character(variableMetadata$name),"_") |
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130 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) }) |
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131 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco)) |
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132 variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))]) |
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133 return(variableMetadata) |
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134 } |
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135 |
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136 #@author G. Le Corguille |
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137 # 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 |
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155 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax)) |
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156 for (i in 1:nrow(featureDefinitions(xdata))) { |
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157 mzmin = featureDefinitions(xdata)[i,]$mzmin |
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158 mzmax = featureDefinitions(xdata)[i,]$mzmax |
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159 plotChromPeakDensity(xdata, param = param, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit))) |
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160 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1) |
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161 } |
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162 |
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163 dev.off() |
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164 } |
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165 |
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166 #@author G. Le Corguille |
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167 # Draw the plotChromPeakDensity 3 per page in a pdf file |
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168 getPlotAdjustedRtime <- function(xdata) { |
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169 |
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170 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12) |
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171 |
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172 # Color by group |
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173 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1") |
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174 if (length(group_colors) > 1) { |
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175 names(group_colors) <- unique(xdata$sample_group) |
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176 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group]) |
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177 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1) |
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178 } |
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179 |
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180 # Color by sample |
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181 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name))) |
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182 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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183 |
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184 dev.off() |
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185 } |
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186 |
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187 #@author G. Le Corguille |
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188 # value: intensity values to be used into, maxo or intb |
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189 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, naTOzero=T, variableMetadataOutput, dataMatrixOutput, sampleNamesList) { |
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190 dataMatrix <- featureValues(xdata, method="medret", value=intval) |
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191 colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix))) |
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192 dataMatrix = cbind(name=groupnames(xdata), dataMatrix) |
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193 variableMetadata <- featureDefinitions(xdata) |
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194 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt" |
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195 variableMetadata = data.frame(name=groupnames(xdata), variableMetadata) |
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196 |
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197 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute) |
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198 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ) |
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199 dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero) |
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200 |
19
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201 # FIX: issue when the vector at peakidx is too long and is written in a new line during the export |
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202 variableMetadata[,"peakidx"] <- vapply(variableMetadata[,"peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",") |
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203 |
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204 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F) |
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205 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F) |
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206 |
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207 } |
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208 |
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209 #@author G. Le Corguille |
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210 # It allow different of field separators |
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211 getDataFrameFromFile <- function(filename, header=T) { |
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212 myDataFrame <- read.table(filename, header=header, sep=";", stringsAsFactors=F) |
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213 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep="\t", stringsAsFactors=F) |
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214 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep=",", stringsAsFactors=F) |
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215 if (ncol(myDataFrame) < 2) { |
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216 error_message="Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation" |
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217 print(error_message) |
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218 stop(error_message) |
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219 } |
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220 return(myDataFrame) |
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221 } |
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222 |
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223 #@author G. Le Corguille |
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224 # Draw the BPI and TIC graphics |
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225 # colored by sample names or class names |
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226 getPlotChromatogram <- function(chrom, xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") { |
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227 |
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228 if (aggregationFun == "sum") |
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229 type="Total Ion Chromatograms" |
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230 else |
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231 type="Base Peak Intensity Chromatograms" |
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232 |
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233 adjusted="Raw" |
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234 if (hasAdjustedRtime(xdata)) |
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235 adjusted="Adjusted" |
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236 |
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237 main <- paste(type,":",adjusted,"data") |
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238 |
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239 pdf(pdfname, width=16, height=10) |
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240 |
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241 # Color by group |
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242 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1") |
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243 if (length(group_colors) > 1) { |
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244 names(group_colors) <- unique(xdata$sample_group) |
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245 plot(chrom, col = group_colors[as.factor(chrom$sample_group)], main=main, peakType = "none") |
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246 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1) |
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247 } |
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248 |
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249 # Color by sample |
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250 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main, peakType = "none") |
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251 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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252 |
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253 dev.off() |
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254 } |
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255 |
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256 |
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257 # Get the polarities from all the samples of a condition |
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258 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM |
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259 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM |
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260 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") { |
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261 cat("Creating the sampleMetadata file...\n") |
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262 |
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263 #Create the sampleMetada dataframe |
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264 sampleMetadata <- xdata@phenoData@data |
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265 rownames(sampleMetadata) <- NULL |
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266 colnames(sampleMetadata) <- c("sample_name", "class") |
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267 |
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268 sampleNamesOrigin <- sampleMetadata$sample_name |
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269 sampleNamesMakeNames <- make.names(sampleNamesOrigin) |
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270 |
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271 if (any(duplicated(sampleNamesMakeNames))) { |
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272 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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273 for (sampleName in sampleNamesOrigin) { |
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274 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr()) |
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275 } |
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276 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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277 } |
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278 |
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279 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) { |
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280 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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281 for (sampleName in sampleNamesOrigin) { |
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282 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n")) |
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283 } |
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284 } |
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285 |
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286 sampleMetadata$sample_name <- sampleNamesMakeNames |
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287 |
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288 |
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289 #For each sample file, the following actions are done |
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290 for (fileIdx in 1:length(fileNames(xdata))) { |
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291 #Check if the file is in the CDF format |
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292 if (!mzR:::netCDFIsFile(fileNames(xdata))) { |
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293 |
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294 # If the column isn't exist, with add one filled with NA |
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295 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA |
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296 |
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297 #Extract the polarity (a list of polarities) |
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298 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"] |
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299 #Verify if all the scans have the same polarity |
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300 uniq_list <- unique(polarity) |
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301 if (length(uniq_list)>1){ |
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302 polarity <- "mixed" |
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303 } else { |
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304 polarity <- as.character(uniq_list) |
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305 } |
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306 |
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307 #Set the polarity attribute |
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308 sampleMetadata$polarity[fileIdx] <- polarity |
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309 } |
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310 |
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311 } |
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312 |
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313 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput) |
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314 |
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315 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames)) |
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316 |
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317 } |
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318 |
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319 |
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320 # This function will compute MD5 checksum to check the data integrity |
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321 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr |
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322 getMd5sum <- function (files) { |
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323 cat("Compute md5 checksum...\n") |
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324 library(tools) |
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325 return(as.matrix(md5sum(files))) |
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326 } |
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327 |
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328 # This function retrieve the raw file in the working directory |
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329 # - if zipfile: unzip the file with its directory tree |
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330 # - if singlefiles: set symlink with the good filename |
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331 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr |
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332 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile, args, prefix="") { |
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333 |
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334 if (!(prefix %in% c("","Positive","Negative","MS1","MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'") |
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335 |
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336 # single - if the file are passed in the command arguments -> refresh singlefile |
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337 if (!is.null(args[[paste0("singlefile_galaxyPath",prefix)]])) { |
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338 singlefile_galaxyPaths <- unlist(strsplit(args[[paste0("singlefile_galaxyPath",prefix)]],"\\|")) |
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339 singlefile_sampleNames <- unlist(strsplit(args[[paste0("singlefile_sampleName",prefix)]],"\\|")) |
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340 |
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341 singlefile <- NULL |
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342 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) { |
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343 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i] |
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344 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i] |
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345 # In case, an url is used to import data within Galaxy |
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346 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1) |
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347 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath |
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348 } |
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349 } |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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350 # zipfile - if the file are passed in the command arguments -> refresh zipfile |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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351 if (!is.null(args[[paste0("zipfile",prefix)]])) |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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352 zipfile <- args[[paste0("zipfile",prefix)]] |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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353 |
acc66e5c23d7
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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354 # single |
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355 if(!is.null(singlefile) && (length("singlefile")>0)) { |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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356 files <- vector() |
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357 for (singlefile_sampleName in names(singlefile)) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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358 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]] |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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359 if(!file.exists(singlefile_galaxyPath)){ |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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360 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!") |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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361 print(error_message); stop(error_message) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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362 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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363 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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364 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T))) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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365 file.copy(singlefile_galaxyPath, singlefile_sampleName) |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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366 files <- c(files, singlefile_sampleName) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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367 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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368 } |
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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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369 # zipfile |
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370 if(!is.null(zipfile) && (zipfile != "")) { |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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371 if(!file.exists(zipfile)){ |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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372 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!") |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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373 print(error_message) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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374 stop(error_message) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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375 } |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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376 suppressWarnings(unzip(zipfile, unzip="unzip")) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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377 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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378 #get the directory name |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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379 suppressWarnings(filesInZip <- unzip(zipfile, list=T)) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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380 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1]))) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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381 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir] |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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382 directory <- "." |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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383 if (length(directories) == 1) directory <- directories |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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384 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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385 cat("files_root_directory\t",directory,"\n") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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386 |
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387 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") |
acc66e5c23d7
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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388 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|") |
acc66e5c23d7
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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389 info <- file.info(directory) |
acc66e5c23d7
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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390 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE) |
acc66e5c23d7
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391 files <- c(directory[!info$isdir], listed) |
acc66e5c23d7
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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392 exists <- file.exists(files) |
acc66e5c23d7
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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393 files <- files[exists] |
acc66e5c23d7
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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394 |
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395 } |
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396 return(list(zipfile=zipfile, singlefile=singlefile, files=files)) |
acc66e5c23d7
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397 |
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398 } |
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399 |
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400 |
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401 # This function retrieve a xset like object |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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402 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr |
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403 getxcmsSetObject <- function(xobject) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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404 # XCMS 1.x |
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405 if (class(xobject) == "xcmsSet") |
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406 return (xobject) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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407 # XCMS 3.x |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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408 if (class(xobject) == "XCMSnExp") { |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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409 # Get the legacy xcmsSet object |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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410 suppressWarnings(xset <- as(xobject, 'xcmsSet')) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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411 if (!is.null(xset@phenoData$sample_group)) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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412 sampclass(xset) <- xset@phenoData$sample_group |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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413 else |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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414 sampclass(xset) <- "." |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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415 return (xset) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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416 } |
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417 } |