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annotate chipseeker.R @ 1:95f779f4adb7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
author rnateam
date Tue, 29 May 2018 15:08:04 -0400
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children 535321abf9a4
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95f779f4adb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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1 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
95f779f4adb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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95f779f4adb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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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 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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95f779f4adb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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6 suppressPackageStartupMessages({
95f779f4adb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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7 library(ChIPseeker)
95f779f4adb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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8 library(GenomicFeatures)
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9 library(optparse)
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10 })
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11
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12 option_list <- list(
95f779f4adb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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13 make_option(c("-i","--infile"), type="character", help="Peaks file to be annotated"),
95f779f4adb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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14 make_option(c("-G","--gtf"), type="character", help="GTF to create TxDb."),
95f779f4adb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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15 make_option(c("-u","--upstream"), type="integer", help="TSS upstream region"),
95f779f4adb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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16 make_option(c("-d","--downstream"), type="integer", help="TSS downstream region"),
95f779f4adb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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17 make_option(c("-F","--flankgeneinfo"), type="logical", help="Add flanking gene info"),
95f779f4adb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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18 make_option(c("-D","--flankgenedist"), type="integer", help="Flanking gene distance"),
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19 make_option(c("-f","--format"), type="character", help="Output format (interval or tabular)."),
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20 make_option(c("-p","--plots"), type="character", help="PDF of plots.")
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21 )
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23 parser <- OptionParser(usage = "%prog [options] file", option_list=option_list)
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24 args = parse_args(parser)
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26 peaks = args$infile
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27 gtf = args$gtf
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28 up = args$upstream
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29 down = args$downstream
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30 format = args$format
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31 plots = args$plots
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33 peaks <- readPeakFile(peaks)
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35 # Make TxDb from GTF
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36 txdb <- makeTxDbFromGFF(gtf, format="gtf")
95f779f4adb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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37 if (!is.null(args$flankgeneinfo)) {
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38 peakAnno <- annotatePeak(peaks, TxDb=txdb, tssRegion=c(-up, down), addFlankGeneInfo=args$flankgeneinfo, flankDistance=args$flankgenedist)
95f779f4adb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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39 } else {
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40 peakAnno <- annotatePeak(peaks, TxDb=txdb, tssRegion=c(-up, down))
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41 }
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43 # Convert from 1-based to 0-based format
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44 res <- as.GRanges(peakAnno)
95f779f4adb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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45 metacols <- mcols(res)
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46 if (format == "interval") {
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47 metacols <- apply(as.data.frame(metacols), 1, function(col) paste(col, collapse="|"))
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48 resout <- data.frame(Chrom=seqnames(res),
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49 Start=start(res) - 1,
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50 End=end(res),
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51 Comment=metacols)
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52 } else {
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53 resout <- data.frame(Chrom=seqnames(res),
95f779f4adb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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54 Start=start(res) - 1,
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55 End=end(res),
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56 metacols)
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57 }
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58
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59 write.table(resout, file="out.tab", sep="\t", row.names=FALSE, quote=FALSE)
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60
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61 if (!is.null(plots)) {
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62 pdf("out.pdf", width=14)
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63 plotAnnoPie(peakAnno)
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64 plotAnnoBar(peakAnno)
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65 vennpie(peakAnno)
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66 upsetplot(peakAnno)
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67 plotDistToTSS(peakAnno, title="Distribution of transcription factor-binding loci\nrelative to TSS")
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68 dev.off()
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69 }