[BioC] countOverlaps() only count positive strand (from GenomicRanges example)
jasonlu68 at gmail.com
Mon Dec 13 20:22:18 CET 2010
Song Li <songli116 at ...> writes:
> Hi Martin and Vincent,
> Thank you for your replies, here is my code:
> > strand(exonRanges)<-"*"
> Error in `strand<-`(`*tmp*`, value = "*") :
> replacement 'value' is not an AtomicList with the same elementLengths as 'x'
> > levels(strand(aligns))<-c('*','*','*')
> Error in function (classes, fdef, mtable) :
> unable to find an inherited method for function "strand<-", for
> signature "GappedAlignments"
> It does not seem to be that straightforward.
> I have been searching for ways to make modification to the
> GappedAlignments and GRangesList objects.
I just encountered the same problem.
What I did is this
aln <- grg(readBamGappedAlignments(bam))
strand(aln) = "*"
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