Mercurial > repos > bgruening > diffbind
comparison diffbind.R @ 9:6171163112de draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
author | iuc |
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date | Sun, 28 Jan 2018 05:10:25 -0500 |
parents | |
children | d7725c5596ab |
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8:a2bb4f5252a8 | 9:6171163112de |
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1 ## Setup R error handling to go to stderr | |
2 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) | |
3 # we need that to not crash galaxy with an UTF8 error on German LC settings. | |
4 Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") | |
5 | |
6 suppressPackageStartupMessages({ | |
7 library('getopt') | |
8 library('DiffBind') | |
9 }) | |
10 | |
11 options(stringAsfactors = FALSE, useFancyQuotes = FALSE) | |
12 args <- commandArgs(trailingOnly = TRUE) | |
13 | |
14 #get options, using the spec as defined by the enclosed list. | |
15 #we read the options from the default: commandArgs(TRUE). | |
16 spec = matrix(c( | |
17 'verbose', 'v', 2, "integer", | |
18 'help' , 'h', 0, "logical", | |
19 'outfile' , 'o', 1, "character", | |
20 'plots' , 'p', 2, "character", | |
21 'infile' , 'i', 1, "character", | |
22 'format', 'f', 1, "character", | |
23 'th', 't', 1, "double", | |
24 'bmatrix', 'b', 0, "logical" | |
25 ), byrow=TRUE, ncol=4); | |
26 | |
27 opt = getopt(spec); | |
28 | |
29 # if help was asked for print a friendly message | |
30 # and exit with a non-zero error code | |
31 if ( !is.null(opt$help) ) { | |
32 cat(getopt(spec, usage=TRUE)); | |
33 q(status=1); | |
34 } | |
35 | |
36 if ( !is.null(opt$plots) ) { | |
37 pdf(opt$plots) | |
38 } | |
39 | |
40 sample = dba(sampleSheet=opt$infile, peakFormat='bed') | |
41 sample_count = dba.count(sample) | |
42 sample_contrast = dba.contrast(sample_count, categories=DBA_CONDITION, minMembers=2) | |
43 sample_analyze = dba.analyze(sample_contrast) | |
44 diff_bind = dba.report(sample_analyze) | |
45 orvals = dba.plotHeatmap(sample_analyze, contrast=1, correlations=FALSE) | |
46 | |
47 resSorted <- diff_bind[order(diff_bind$FDR),] | |
48 write.table(as.data.frame(resSorted), file = opt$outfile, sep="\t", quote = FALSE, append=TRUE, row.names = FALSE, col.names = FALSE) | |
49 | |
50 # Output binding affinity scores | |
51 if (!is.null(opt$bmatrix)) { | |
52 bmat <- dba.peakset(sample_count, bRetrieve=TRUE, DataType=DBA_DATA_FRAME) | |
53 write.table(as.data.frame(bmat), file="bmatrix.tab", sep="\t", quote=FALSE, row.names=FALSE, col.names=FALSE) | |
54 } | |
55 | |
56 dev.off() | |
57 sessionInfo() |