Mercurial > repos > bgruening > diffbind

comparison diffbind.R @ 9:20c431b4cf74 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bgruening
date Tue, 14 Jan 2014 18:07:20 -0500
parents fa67bcb732f6
children b1b96b6ed60c
comparison
equal deleted inserted replaced
8:7929c8b3f6f9 9:20c431b4cf74
21 opt = getopt(spec); 21 opt = getopt(spec);
22 22
23 # if help was asked for print a friendly message 23 # if help was asked for print a friendly message
24 # and exit with a non-zero error code 24 # and exit with a non-zero error code
25 if ( !is.null(opt$help) ) { 25 if ( !is.null(opt$help) ) {
26 cat(getopt(spec, usage=TRUE)); 26 cat(getopt(spec, usage=TRUE));
27 q(status=1); 27 q(status=1);
28 } 28 }
29 29
30 30
31 library('DiffBind') 31 library('DiffBind')
32 # used to save to BED, GFF or WIG format 32 # used to save to BED, GFF or WIG format
33 library('rtracklayer') 33 library('rtracklayer')
34 34
35 if ( !is.null(opt$plots) ) { 35 if ( !is.null(opt$plots) ) {
36 pdf(opt$plots) 36 pdf(opt$plots)
37 } 37 }
38 38
39 39
40 sample = dba(sampleSheet=opt$infile) 40 sample = dba(sampleSheet=opt$infile, peakFormat='bed')
41 sample_count = dba.count(sample) 41 sample_count = dba.count(sample)
42 sample_contrast = dba.contrast(sample_count, categories=DBA_CONDITION) 42 sample_contrast = dba.contrast(sample_count, categories=DBA_CONDITION)
43 sample_analyze = dba.analyze(sample_contrast) 43 sample_analyze = dba.analyze(sample_contrast)
44 diff_bind = dba.report(sample_analyze) 44 diff_bind = dba.report(sample_analyze)
45 45