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annotate diffbind.R @ 11:4c7ab9995f9e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
author iuc
date Sat, 07 Apr 2018 15:45:41 -0400
parents d7725c5596ab
children 1de83981d43c
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6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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1 ## Setup R error handling to go to stderr
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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2 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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3 # we need that to not crash galaxy with an UTF8 error on German LC settings.
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4 Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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6 suppressPackageStartupMessages({
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7 library('getopt')
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8 library('DiffBind')
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9 library('rjson')
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10 })
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12 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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13 args <- commandArgs(trailingOnly = TRUE)
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6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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15 #get options, using the spec as defined by the enclosed list.
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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16 #we read the options from the default: commandArgs(TRUE).
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17 spec = matrix(c(
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18 'infile' , 'i', 1, "character",
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19 'outfile' , 'o', 1, "character",
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20 'scorecol', 'n', 1, "integer",
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21 'lowerbetter', 'l', 1, "logical",
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22 'summits', 's', 1, "integer",
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23 'th', 't', 1, "double",
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24 'format', 'f', 1, "character",
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25 'plots' , 'p', 2, "character",
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26 'bmatrix', 'b', 0, "logical",
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27 "rdaOpt", "r", 0, "logical",
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28 'infoOpt' , 'a', 0, "logical",
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29 'verbose', 'v', 2, "integer",
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30 'help' , 'h', 0, "logical"
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31 ), byrow=TRUE, ncol=4);
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33 opt = getopt(spec);
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35 # if help was asked for print a friendly message
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36 # and exit with a non-zero error code
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37 if ( !is.null(opt$help) ) {
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38 cat(getopt(spec, usage=TRUE));
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39 q(status=1);
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40 }
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41
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42 parser <- newJSONParser()
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43 parser$addData(opt$infile)
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44 factorList <- parser$getObject()
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45 filenamesIn <- unname(unlist(factorList[[1]][[2]]))
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46 peaks <- filenamesIn[grepl("peaks.bed", filenamesIn)]
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47 bams <- filenamesIn[grepl("bamreads.bam", filenamesIn)]
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48 ctrls <- filenamesIn[grepl("bamcontrol.bam", filenamesIn)]
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
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49
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50 # get the group and sample id from the peaks filenames
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51 groups <- sapply(strsplit(peaks,"-"), `[`, 1)
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52 samples <- sapply(strsplit(peaks,"-"), `[`, 2)
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54 if ( length(ctrls) != 0 ) {
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55 sampleTable <- data.frame(SampleID=samples,
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56 Condition=groups,
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57 bamReads=bams,
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58 bamControl=ctrls,
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59 Peaks=peaks,
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60 Tissue=samples, # using "Tissue" column to display ids as labels in PCA plot
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61 stringsAsFactors=FALSE)
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62 } else {
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63 sampleTable <- data.frame(SampleID=samples,
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64 Replicate=samples,
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65 Condition=groups,
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66 bamReads=bams,
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67 Peaks=peaks,
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68 Tissue=samples,
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69 stringsAsFactors=FALSE)
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70 }
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71
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72 sample = dba(sampleSheet=sampleTable, peakFormat='bed', scoreCol=opt$scorecol, bLowerScoreBetter=opt$lowerbetter)
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74 if ( !is.null(opt$summits) ) {
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75 sample_count = dba.count(sample, summits=opt$summits)
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76 } else {
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77 sample_count = dba.count(sample)
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78 }
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79
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80 sample_contrast = dba.contrast(sample_count, categories=DBA_CONDITION, minMembers=2)
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81 sample_analyze = dba.analyze(sample_contrast)
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82 diff_bind = dba.report(sample_analyze, th=opt$th)
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83
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84 # Generate plots
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85 if ( !is.null(opt$plots) ) {
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86 pdf(opt$plots)
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87 orvals = dba.plotHeatmap(sample_analyze, contrast=1, correlations=FALSE, cexCol=0.8, th=opt$th)
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88 dba.plotPCA(sample_analyze, contrast=1, th=opt$th, label=DBA_TISSUE, labelSize=0.3)
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89 dba.plotMA(sample_analyze, th=opt$th)
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90 dba.plotVolcano(sample_analyze, th=opt$th)
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91 dba.plotBox(sample_analyze, th=opt$th)
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92 dev.off()
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93 }
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94
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95 # Output differential binding sites
9
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96 resSorted <- diff_bind[order(diff_bind$FDR),]
11
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97 write.table(as.data.frame(resSorted), file = opt$outfile, sep="\t", quote = FALSE, append=TRUE, row.names = FALSE)
9
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98
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99 # Output binding affinity scores
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100 if (!is.null(opt$bmatrix)) {
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101 bmat <- dba.peakset(sample_count, bRetrieve=TRUE, DataType=DBA_DATA_FRAME)
11
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102 write.table(as.data.frame(bmat), file="bmatrix.tab", sep="\t", quote=FALSE, row.names=FALSE)
9
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103 }
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104
11
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105 # Output RData file
10
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106 if (!is.null(opt$rdaOpt)) {
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107 save.image(file = "DiffBind_analysis.RData")
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108 }
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109
11
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110 # Output analysis info
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111 if (!is.null(opt$infoOpt)) {
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112 info <- "DiffBind_analysis_info.txt"
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113 cat("dba.count Info\n\n", file=info, append = TRUE)
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114 capture.output(sample, file=info, append=TRUE)
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115 cat("\ndba.analyze Info\n\n", file=info, append = TRUE)
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
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116 capture.output(sample_analyze, file=info, append=TRUE)
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117 cat("\nSessionInfo\n\n", file=info, append = TRUE)
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118 capture.output(sessionInfo(), file=info, append=TRUE)
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119 }