[Bioc-devel] mapping between original and reduced ranges

Cook, Malcolm MEC at stowers.org
Wed Mar 14 20:46:58 CET 2012

Chiming in....

on a similar note....

A version of `disjoin` which returns a Hits/RangesMapping additional to the GRanges result would be most useful  and probably not require much additional effort (assuming `disjoin` computes this internally)

Of course, it is easy to live without since I can just perform the findOverlaps myself after the disjoin.... it just "feels wrong" (tm)



> -----Original Message-----
> From: bioc-devel-bounces at r-project.org [mailto:bioc-devel-bounces at r-
> project.org] On Behalf Of Hahne, Florian
> Sent: Wednesday, March 14, 2012 2:22 PM
> To: bioc-devel at r-project.org
> Subject: [Bioc-devel] mapping between original and reduced ranges
> This bounced before, guess the mailing list does not like HTML mails. So
> one more try:
> I had the following offline discussion with Michael about how one could
> retain a mapping of the ranges in a GRanges object before and after
> reduce. He suggested to take it to the list. Is that something that could
> be added to GenomicRanges/IRanges?
> Florian
> I have a slightly tricky application for which I need to reduce a GRanges
> object, but I would like to be able to process some of the original
> elementMetadata of the merged ranges later. The only way I was able to
> figure out which of the original ranges correspond to the merged ranges
> was to perform a findOverlaps operation, but of course that is rather
> costly. Is there a way to get the merge information out of the original
> reduce call?
> Here is a brief example:
> gr <- GRanges(seqnames="chr1", ranges=IRanges(start=c(1,6,12,24,27),
> width=5), foo=1:5, bar=letters[1:5])
> gr2 <- reduce(gr, min.gapwidth=1)
> ind <- queryHits(findOverlaps(gr2, gr))
> split(values(gr), ind)
> Unfortunately, this is the idiom. I could see an improvement where reduce
> or a similarly named function would return a Hits object (in addition to
> the actual reduce result) that would indicate the mapping between the
> input and reduced ranges. The RangesMapping structure would be really
> close to what we would need.
> Michael
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