You can generate bed files from a
GRanges object (as returned by
export.bed() from the
> library(rtracklayer) > dbsites <- dba.report(myDBA, contrast=1, th=0.05) > export.bed(dbsites,"dbsites.bed")
I've a slightly more complicated version of this issue. I want to export a list of peaks that do not overlap within 4 groups (e.g. myDBA$onlyA or myDBA$AandC).
From dba.analyze I have 6 contrasts. Which options do I use for dba.report to generate a contrast resembling:
myDBA.OL <- dba.overlap(myDBA, myDBA$masks$Consensus)
so I can export these subsets as .bed?