Mercurial > repos > bgruening > diffbind

annotate diffbind.R @ 7:681dedc42aca draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
1 ## Setup R error handling to go to stderr
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
2 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
3 # we need that to not crash galaxy with an UTF8 error on German LC settings.
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
4 Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
5
7
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 1
diff changeset
6 suppressPackageStartupMessages({
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 1
diff changeset
7 library('getopt')
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 1
diff changeset
8 library('DiffBind')
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 1
diff changeset
9 })
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 1
diff changeset
10
0
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
11 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
12 args <- commandArgs(trailingOnly = TRUE)
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
13
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
14 #get options, using the spec as defined by the enclosed list.
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
15 #we read the options from the default: commandArgs(TRUE).
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
16 spec = matrix(c(
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
17 'verbose', 'v', 2, "integer",
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
18 'help' , 'h', 0, "logical",
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
19 'outfile' , 'o', 1, "character",
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
20 'plots' , 'p', 2, "character",
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
21 'infile' , 'i', 1, "character",
7
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 1
diff changeset
22 'format', 'f', 1, "character",
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 1
diff changeset
23 'th', 't', 1, "double",
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 1
diff changeset
24 'bmatrix', 'b', 0, "logical"
0
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
25 ), byrow=TRUE, ncol=4);
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
26
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
27 opt = getopt(spec);
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
28
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
29 # if help was asked for print a friendly message
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
30 # and exit with a non-zero error code
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
31 if ( !is.null(opt$help) ) {
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
32 cat(getopt(spec, usage=TRUE));
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
33 q(status=1);
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
34 }
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
35
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
36 if ( !is.null(opt$plots) ) {
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
37 pdf(opt$plots)
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
38 }
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
39
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
40 sample = dba(sampleSheet=opt$infile, peakFormat='bed')
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
41 sample_count = dba.count(sample)
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
42 sample_contrast = dba.contrast(sample_count, categories=DBA_CONDITION, minMembers=2)
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
43 sample_analyze = dba.analyze(sample_contrast)
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
44 diff_bind = dba.report(sample_analyze)
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
45 orvals = dba.plotHeatmap(sample_analyze, contrast=1, correlations=FALSE)
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
46
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
47 resSorted <- diff_bind[order(diff_bind$FDR),]
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
48 write.table(as.data.frame(resSorted), file = opt$outfile, sep="\t", quote = FALSE, append=TRUE, row.names = FALSE, col.names = FALSE)
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
49
7
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 1
diff changeset
50 # Output binding affinity scores
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 1
diff changeset
51 if (!is.null(opt$bmatrix)) {
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 1
diff changeset
52 bmat <- dba.peakset(sample_count, bRetrieve=TRUE, DataType=DBA_DATA_FRAME)
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 1
diff changeset
53 write.table(as.data.frame(bmat), file="bmatrix.tab", sep="\t", quote=FALSE, row.names=FALSE, col.names=FALSE)
681dedc42aca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 1
diff changeset
54 }
0
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
55
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
56 dev.off()
7faaf4a5e4e1 Uploaded
bgruening
parents:
diff changeset
57 sessionInfo()