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annotate dexseq.R @ 5:278b189248cd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
author iuc
date Mon, 14 Jan 2019 05:02:19 -0500
parents 6e8b61c54ff3
children 62adf13b86ea
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4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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1 ## Setup R error handling to go to stderr
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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2 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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3 # we need that to not crash galaxy with an UTF8 error on German LC settings.
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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4 Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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5
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6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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6 suppressPackageStartupMessages({
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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7 library("DEXSeq")
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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8 library('getopt')
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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9 library('rjson')
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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10 })
0
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4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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13 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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14 args <- commandArgs(trailingOnly = TRUE)
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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16 #get options, using the spec as defined by the enclosed list.
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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17 #we read the options from the default: commandArgs(TRUE).
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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18 spec = matrix(c(
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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19 'verbose', 'v', 2, "integer",
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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20 'help', 'h', 0, "logical",
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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21 'gtf', 'a', 1, "character",
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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22 'outfile', 'o', 1, "character",
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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23 'reportdir', 'r', 1, "character",
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278b189248cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
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24 'rds', 'd', 1, "character",
0
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25 'factors', 'f', 1, "character",
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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26 'threads', 'p', 1, "integer",
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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27 'fdr', 'c', 1, "double"
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28 ), byrow=TRUE, ncol=4);
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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29 opt = getopt(spec);
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31 # if help was asked for print a friendly message
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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32 # and exit with a non-zero error code
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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33 if ( !is.null(opt$help) ) {
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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34 cat(getopt(spec, usage=TRUE));
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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35 q(status=1);
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36 }
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38 trim <- function (x) gsub("^\\s+|\\s+$", "", x)
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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39 opt$samples <- trim(opt$samples)
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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40 opt$factors <- trim(opt$factors)
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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42 parser <- newJSONParser()
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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43 parser$addData( opt$factors )
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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44 factorsList <- parser$getObject()
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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46 sampleTable<-data.frame()
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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47 countFiles<-c()
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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48 factorNames<-c()
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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49 primaryFactor<-""
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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50 for(factor in factorsList){
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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51 factorName<-factor[[1]]
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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52 factorNames<-append(factorNames, paste(factorName,"exon",sep=":"))
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53 factorValuesMapList<-factor[[2]]
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54 c = length(factorValuesMapList)
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55 for (factorValuesMap in factorValuesMapList){
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56 for(files in factorValuesMap){
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57 for(file in files){
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58 if(primaryFactor == "") {
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59 countFiles<-append(countFiles,file)
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60 }
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61 sampleTable[basename(file),factorName]<-paste(c,names(factorValuesMap),sep="_")
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62 }
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63 }
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64 c = c-1
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65 }
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66 if(primaryFactor == ""){
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67 primaryFactor <- factorName
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68 }
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69 }
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70
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71 factorNames<-append(factorNames,"exon")
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72 factorNames<-append(factorNames,"sample")
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73 factorNames<-rev(factorNames)
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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74 formulaFullModel <- as.formula(paste("", paste(factorNames, collapse=" + "), sep=" ~ "))
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75 factorNames <- head(factorNames,-1)
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76 formulaReducedModel <- as.formula(paste("", paste(factorNames, collapse=" + "), sep=" ~ "))
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77
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78 sampleTable
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79 formulaFullModel
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80 formulaReducedModel
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81 primaryFactor
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82 countFiles
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83 opt$reportdir
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84 opt$threads
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85 getwd()
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86
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87 dxd = DEXSeqDataSetFromHTSeq(countFiles, sampleData=sampleTable, design= formulaFullModel, flattenedfile=opt$gtf)
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88
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89 colData(dxd)
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90 dxd <- estimateSizeFactors(dxd)
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91 print("Estimated size factors")
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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92 sizeFactors(dxd)
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93 BPPARAM=MulticoreParam(workers=opt$threads)
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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94 dxd <- estimateDispersions(dxd, formula=formulaFullModel, BPPARAM=BPPARAM)
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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95 print("Estimated dispersions")
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96 dxd <- testForDEU(dxd, reducedModel=formulaReducedModel, fullModel=formulaFullModel, BPPARAM=BPPARAM)
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4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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97 print("tested for DEU")
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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98 dxd <- estimateExonFoldChanges(dxd, fitExpToVar=primaryFactor, BPPARAM=BPPARAM)
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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99 print("Estimated fold changes")
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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100 res <- DEXSeqResults(dxd)
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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101 print("Results")
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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102 table(res$padj <= opt$fdr)
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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103 resSorted <- res[order(res$padj),]
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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104 head(resSorted)
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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105
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106 export_table <- as.data.frame(resSorted)
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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107 last_column <- ncol(export_table)
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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108 for(i in 1:nrow(export_table)) {
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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109 export_table[i,last_column] <- paste(export_table[i,last_column][[1]],collapse=", ")
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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110 }
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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111 write.table(export_table, file = opt$outfile, sep="\t", quote = FALSE, col.names = FALSE)
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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112 print("Written Results")
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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113
5
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114 if ( !is.null(opt$rds) ) {
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115 saveRDS(res, file="DEXSeqResults.rds")
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116 }
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117
0
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118 if ( !is.null(opt$reportdir) ) {
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119 DEXSeqHTML(res, fitExpToVar=primaryFactor, path=opt$reportdir, FDR=opt$fdr, color=c("#B7FEA0", "#FF8F43", "#637EE9", "#FF0000", "#F1E7A1", "#C3EEE7","#CEAEFF", "#EDC3C5", "#AAA8AA"))
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120 }
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121 sessionInfo()