comparison diffbind.R @ 10:b1b96b6ed60c draft

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9:20c431b4cf74

}


library('DiffBind')
# used to save to BED, GFF or WIG format
library('rtracklayer')

if ( !is.null(opt$plots) ) {
    pdf(opt$plots)
}


sample = dba(sampleSheet=opt$infile, peakFormat='bed')
sample_count = dba.count(sample)
sample_contrast = dba.contrast(sample_count, categories=DBA_CONDITION)
sample_analyze = dba.analyze(sample_contrast)
diff_bind = dba.report(sample_analyze)


export(diff_bind, opt$outfile, format=opt$format)

dev.off()
sessionInfo()

10:b1b96b6ed60c

}


library('DiffBind')
# used to save to BED, GFF or WIG format

if ( !is.null(opt$plots) ) {
    pdf(opt$plots)
}


sample = dba(sampleSheet=opt$infile, peakFormat='bed')
sample_count = dba.count(sample)
sample_contrast = dba.contrast(sample_count, categories=DBA_CONDITION, minMembers=2)
sample_analyze = dba.analyze(sample_contrast)
diff_bind = dba.report(sample_analyze)
orvals = dba.plotHeatmap(sample_analyze, contrast=1, correlations=FALSE)

resSorted <- diff_bind[order(diff_bind$FDR),]
write.table(as.data.frame(resSorted), file = opt$outfile, sep="\t", quote = FALSE, append=TRUE, row.names = FALSE, col.names = FALSE)


dev.off()
sessionInfo()