Hi Michael, I think that I expressed myself too ambiguously.
I am looking for the multiple intersection. That is, I am looking for the ranges in A that are even minimally overlapped by ranges in ALL the rest of the RangesData instances. A super-dee-duper intersection. The union() operation would be finding overlaps with ANY of the rest of the RangesData. At the moment, like Karl, I am evading the problem by dint of shameful for loops. Do you think that there is a more elegant way? Thanks Ivan Ivan Gregoretti, PhD National Institute of Diabetes and Digestive and Kidney Diseases National Institutes of Health 5 Memorial Dr, Building 5, Room 205. Bethesda, MD 20892. USA. Phone: 1-301-496-1592 Fax: 1-301-496-9878 On Tue, Mar 16, 2010 at 4:26 PM, Michael Lawrence <[email protected]> wrote: > > > On Tue, Mar 16, 2010 at 12:34 PM, Ivan Gregoretti <[email protected]> > wrote: >> >> Hello everybody, >> >> Say A, B, C, D, .... are all RangedData instances. >> >> How do you come up with the list of ranges in A that have at least >> some overlap with B, C, D, ...? >> >> I want to calculate the multiple intersection ignoring the extent of >> the overlap. >> >> ?findOverlaps does not hint how to recover the ranges from A. >> > > Something like: > ranges(A) %in% union(union(ranges(B), ranges(C)), ranges(D)) > > That syntax is a little verbose. I propose adding some operators to Ranges, > RangesList and RangedData objects. > > "+" for union() > "-" for setdiff() > "!" for gaps() > > Then we could have: > A %in% (B + C + D) > > What do people think? > > >> >> Thank you, >> >> Ivan >> >> >> Ivan Gregoretti, PhD >> National Institute of Diabetes and Digestive and Kidney Diseases >> National Institutes of Health >> 5 Memorial Dr, Building 5, Room 205. >> Bethesda, MD 20892. USA. >> Phone: 1-301-496-1592 >> Fax: 1-301-496-9878 >> >> _______________________________________________ >> Bioc-sig-sequencing mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
