Hi, I wonder if it's worth having some sort of "internal equal" overlap mode for two GRangesLists. This would check not for total equality between e.g. a set of spliced reads and an exonsBy() GRL but instead only check that the internal starts and ends are equal and that the query outer start and end fall inside the subject (indicating a compatible splicing pattern). I have some pretty inefficient code that filters a "within" overlap result to this, but it might be nice to have it inside the infrastructure. Thanks, Michael [[alternative HTML version deleted]]

On Wed, Oct 26, 2011 at 8:33 AM, Michael Lawrence <lawrence.michael at="" gene.com=""> wrote: > Hi, > > I wonder if it's worth having some sort of "internal equal" overlap mode for > two GRangesLists. This would check not for total equality between e.g. a set > of spliced reads and an exonsBy() GRL but instead only check that the > internal starts and ends are equal and that the query outer start and end > fall inside the subject (indicating a compatible splicing pattern). I have > some pretty inefficient code that filters a "within" overlap result to this, > but it might be nice to have it inside the infrastructure. +1 for this suggestion. Sean

Yes, hear, hear I too have what is probably pretty inefficient code in this space. My needs are similar, but perhaps not identical, in that I need I think it comes down to my wanting a 'any' version in addition to a 'within'. My current approach is similarly to filter the result of a findOverlaps(..., 'any') ensuring that the subject / query pairs are identical in the region of overlap (as computed using pintersect). So, I'm happy to hear any progress in this area.... Cheers ~Malcolm > -----Original Message----- > From: bioconductor-bounces at r-project.org [mailto:bioconductor- > bounces at r-project.org] On Behalf Of Michael Lawrence > Sent: Wednesday, October 26, 2011 7:34 AM > To: bioconductor at r-project.org > Subject: [BioC] "internal equal" overlap mode for GRangesList > > Hi, > > I wonder if it's worth having some sort of "internal equal" overlap mode for > two GRangesLists. This would check not for total equality between e.g. a set > of spliced reads and an exonsBy() GRL but instead only check that the > internal starts and ends are equal and that the query outer start and end > fall inside the subject (indicating a compatible splicing pattern). I have > some pretty inefficient code that filters a "within" overlap result to this, > but it might be nice to have it inside the infrastructure. > > Thanks, > Michael > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor