Question: "internal equal" overlap mode for GRangesList
0
gravatar for Michael Lawrence
8.1 years ago by
United States
Michael Lawrence11k 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. Thanks, Michael [[alternative HTML version deleted]]
infrastructure • 424 views
ADD COMMENTlink modified 8.1 years ago by Malcolm Cook1.5k • written 8.1 years ago by Michael Lawrence11k
Answer: "internal equal" overlap mode for GRangesList
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gravatar for Sean Davis
8.1 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
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
ADD COMMENTlink written 8.1 years ago by Sean Davis21k
Answer: "internal equal" overlap mode for GRangesList
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gravatar for Malcolm Cook
8.1 years ago by
Malcolm Cook1.5k
United States
Malcolm Cook1.5k wrote:
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
ADD COMMENTlink written 8.1 years ago by Malcolm Cook1.5k
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