On Fri, Jul 24, 2009 at 7:47 AM, Johannes Waage <[email protected]>wrote:
> Hi all, > > In assigning RNA-seq data to exon-models, I'm looking for a proper overlap > function. Both IRanges and genomeIntervals have overlap functions, but as > far as I can see, these don't have options for contained overlaps, example: > > > |-------Range 1-------] > [----Range 2----] > > IRanges, genomeIntervals: TRUE > Wanted: TRUE > > > |-------Range 1-------] > [----Range 2----] > > > IRanges, genomeIntervals: TRUE > Wanted: FALSE > > Any suggestions are appreciated! > It's fairly easy to filter the overlaps for this condition. To find where an entire query range (in b) overlaps a subject range (in a): ol <- overlap(a, b) width(ranges(ol, a, b)) == width(b) Is this what you wanted? Michael > > Regards, > Johannes Waage, > Uni. of Copenhagen > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
