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comparison diffbind.R @ 7:681dedc42aca draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
author iuc
date Sun, 28 Jan 2018 04:26:11 -0500
parents 9e9f85c20d99
children
comparison
equal deleted inserted replaced
6:6031247f61d4 7:681dedc42aca
1 ## Setup R error handling to go to stderr 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 ) } ) 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. 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") 4 Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
5 5
6 library('getopt'); 6 suppressPackageStartupMessages({
7 library('getopt')
8 library('DiffBind')
9 })
10
7 options(stringAsfactors = FALSE, useFancyQuotes = FALSE) 11 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
8 args <- commandArgs(trailingOnly = TRUE) 12 args <- commandArgs(trailingOnly = TRUE)
9 13
10 #get options, using the spec as defined by the enclosed list. 14 #get options, using the spec as defined by the enclosed list.
11 #we read the options from the default: commandArgs(TRUE). 15 #we read the options from the default: commandArgs(TRUE).
13 'verbose', 'v', 2, "integer", 17 'verbose', 'v', 2, "integer",
14 'help' , 'h', 0, "logical", 18 'help' , 'h', 0, "logical",
15 'outfile' , 'o', 1, "character", 19 'outfile' , 'o', 1, "character",
16 'plots' , 'p', 2, "character", 20 'plots' , 'p', 2, "character",
17 'infile' , 'i', 1, "character", 21 'infile' , 'i', 1, "character",
18 'format', 'f', 1, 'character' 22 'format', 'f', 1, "character",
23 'th', 't', 1, "double",
24 'bmatrix', 'b', 0, "logical"
19 ), byrow=TRUE, ncol=4); 25 ), byrow=TRUE, ncol=4);
20 26
21 opt = getopt(spec); 27 opt = getopt(spec);
22 28
23 # if help was asked for print a friendly message 29 # if help was asked for print a friendly message
25 if ( !is.null(opt$help) ) { 31 if ( !is.null(opt$help) ) {
26 cat(getopt(spec, usage=TRUE)); 32 cat(getopt(spec, usage=TRUE));
27 q(status=1); 33 q(status=1);
28 } 34 }
29 35
30 library('DiffBind')
31
32 if ( !is.null(opt$plots) ) { 36 if ( !is.null(opt$plots) ) {
33 pdf(opt$plots) 37 pdf(opt$plots)
34 } 38 }
35
36 39
37 sample = dba(sampleSheet=opt$infile, peakFormat='bed') 40 sample = dba(sampleSheet=opt$infile, peakFormat='bed')
38 sample_count = dba.count(sample) 41 sample_count = dba.count(sample)
39 sample_contrast = dba.contrast(sample_count, categories=DBA_CONDITION, minMembers=2) 42 sample_contrast = dba.contrast(sample_count, categories=DBA_CONDITION, minMembers=2)
40 sample_analyze = dba.analyze(sample_contrast) 43 sample_analyze = dba.analyze(sample_contrast)
42 orvals = dba.plotHeatmap(sample_analyze, contrast=1, correlations=FALSE) 45 orvals = dba.plotHeatmap(sample_analyze, contrast=1, correlations=FALSE)
43 46
44 resSorted <- diff_bind[order(diff_bind$FDR),] 47 resSorted <- diff_bind[order(diff_bind$FDR),]
45 write.table(as.data.frame(resSorted), file = opt$outfile, sep="\t", quote = FALSE, append=TRUE, row.names = FALSE, col.names = FALSE) 48 write.table(as.data.frame(resSorted), file = opt$outfile, sep="\t", quote = FALSE, append=TRUE, row.names = FALSE, col.names = FALSE)
46 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 }
47 55
48 dev.off() 56 dev.off()
49 sessionInfo() 57 sessionInfo()