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annotate dexseq.R @ 3:f89c9b25feb4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit e785d126b23609208b055fb8902f3b9368e9b839
author iuc
date Sat, 28 Jul 2018 03:44:02 -0400
parents 6e8b61c54ff3
children 278b189248cd
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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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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')
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9 library('rjson')
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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",
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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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24 '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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25 '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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26 'fdr', 'c', 1, "double"
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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27 ), 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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28 opt = getopt(spec);
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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29
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30 # 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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31 # 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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32 if ( !is.null(opt$help) ) {
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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33 cat(getopt(spec, usage=TRUE));
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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34 q(status=1);
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35 }
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36
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37 trim <- function (x) gsub("^\\s+|\\s+$", "", x)
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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38 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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39 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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41 parser <- newJSONParser()
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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42 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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43 factorsList <- parser$getObject()
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45 sampleTable<-data.frame()
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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46 countFiles<-c()
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47 factorNames<-c()
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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48 primaryFactor<-""
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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49 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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50 factorName<-factor[[1]]
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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51 factorNames<-append(factorNames, paste(factorName,"exon",sep=":"))
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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52 factorValuesMapList<-factor[[2]]
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53 c = length(factorValuesMapList)
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54 for (factorValuesMap in factorValuesMapList){
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55 for(files in factorValuesMap){
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56 for(file in files){
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57 if(primaryFactor == "") {
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58 countFiles<-append(countFiles,file)
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59 }
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60 sampleTable[basename(file),factorName]<-paste(c,names(factorValuesMap),sep="_")
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61 }
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62 }
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63 c = c-1
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64 }
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65 if(primaryFactor == ""){
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66 primaryFactor <- factorName
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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67 }
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68 }
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69
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70 factorNames<-append(factorNames,"exon")
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71 factorNames<-append(factorNames,"sample")
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72 factorNames<-rev(factorNames)
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73 formulaFullModel <- as.formula(paste("", paste(factorNames, collapse=" + "), sep=" ~ "))
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74 factorNames <- head(factorNames,-1)
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75 formulaReducedModel <- as.formula(paste("", paste(factorNames, collapse=" + "), sep=" ~ "))
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76
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77 sampleTable
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78 formulaFullModel
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79 formulaReducedModel
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80 primaryFactor
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81 countFiles
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82 opt$reportdir
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83 opt$threads
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84 getwd()
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85
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86 dxd = DEXSeqDataSetFromHTSeq(countFiles, sampleData=sampleTable, design= formulaFullModel, flattenedfile=opt$gtf)
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87
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88 colData(dxd)
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89 dxd <- estimateSizeFactors(dxd)
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90 print("Estimated size factors")
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91 sizeFactors(dxd)
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92 BPPARAM=MulticoreParam(workers=opt$threads)
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93 dxd <- estimateDispersions(dxd, formula=formulaFullModel, BPPARAM=BPPARAM)
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94 print("Estimated dispersions")
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95 dxd <- testForDEU(dxd, reducedModel=formulaReducedModel, fullModel=formulaFullModel, BPPARAM=BPPARAM)
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96 print("tested for DEU")
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97 dxd <- estimateExonFoldChanges(dxd, fitExpToVar=primaryFactor, BPPARAM=BPPARAM)
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98 print("Estimated fold changes")
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99 res <- DEXSeqResults(dxd)
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100 print("Results")
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101 table(res$padj <= opt$fdr)
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102 resSorted <- res[order(res$padj),]
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103 head(resSorted)
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104
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105 export_table <- as.data.frame(resSorted)
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106 last_column <- ncol(export_table)
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107 for(i in 1:nrow(export_table)) {
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108 export_table[i,last_column] <- paste(export_table[i,last_column][[1]],collapse=", ")
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109 }
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110 write.table(export_table, file = opt$outfile, sep="\t", quote = FALSE, col.names = FALSE)
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111 print("Written Results")
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112
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113 if ( !is.null(opt$reportdir) ) {
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114 save(dxd, resSorted, file = file.path(opt$reportdir,"DEXSeq_analysis.RData"))
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115 save.image()
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116 DEXSeqHTML(res, fitExpToVar=primaryFactor, path=opt$reportdir, FDR=opt$fdr, color=c("#B7FEA0", "#FF8F43", "#637EE9", "#FF0000", "#F1E7A1", "#C3EEE7","#CEAEFF", "#EDC3C5", "#AAA8AA"))
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117 unlink(file.path(opt$reportdir,"DEXSeq_analysis.RData"))
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118 }
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119 sessionInfo()