On Mon, Nov 12, 2012 at 4:28 PM, Michael Lawrence <lawrence.michael at="" gene.com=""> wrote: > > > On Mon, Nov 12, 2012 at 11:00 AM, Kasper Daniel Hansen > <kasperdanielhansen at="" gmail.com=""> wrote: >> >> Hmm, ok. >> >> Well, an alternative is to let the output of pintersect be shorter >> than the two inputs. > > > I would really prefer not to violate that contract of the p* functions. If > there are any empty ranges, it's not easy to figure out how the results > match up with the input. I can see this point of view. But one could use findOverlaps. I am just advocating for my position which is (1) inconsistency with intersect() is not great and (2) I believe I could easily be caught by not noticing a zero-width IRanges. Anyway, reading ?pintersect very carefully, it does discuss these things in some detail, although the paragraph is not consistent with itself (as I read it, it start by saying that an error is thrown if an empty intersect is being produced, but then it contradicts itself later on). Reflecting a bit, I guess I would like a new option for resolve.empty="remove" Kasper > > Michael > >> >> Also, compare to >> intersect(gr1[2], gr2) >> which is empty. >> >> Kasper >> >> >> >> On Mon, Nov 12, 2012 at 1:46 PM, Michael Lawrence >> <lawrence.michael at="" gene.com=""> wrote: >> > The end = start - 1 encoding for zero-width Ranges objects has existed >> > as >> > long as the IRanges package. Having end < start is obviously not ideal, >> > but >> > there are no clearly superior alternatives. >> > >> > Michael >> > >> > >> > On Mon, Nov 12, 2012 at 8:58 AM, Kasper Daniel Hansen >> > <kasperdanielhansen at="" gmail.com=""> wrote: >> >> >> >> Well, I am surprised by the zero width IRanges with start and end. >> >> The choice of start = 5 and end = 4 is - as far as I can see - >> >> completely arbitrary. I also don't like the fact that start() and >> >> end() just reports 5 and 4 - I could see myself making mistakes in my >> >> code, because I believe I assume start <= end. >> >> >> >> But perhaps this is because it is now allowed to have zero-width >> >> IRanges? >> >> >> >> Kasper >> >> >> >> >> >> On Mon, Nov 12, 2012 at 6:20 AM, Vincent Carey >> >> <stvjc at="" channing.harvard.edu=""> wrote: >> >> > does this contradict the doc in some way? the second range of your >> >> > result >> >> > has width zero, which i think is correct. >> >> > >> >> > On Sun, Nov 11, 2012 at 12:16 PM, Kasper Daniel Hansen >> >> > <kasperdanielhansen at="" gmail.com=""> wrote: >> >> >> >> >> >> Example >> >> >> >> >> >> library(GenomicRanges) >> >> >> gr1 = GRanges(seqnames = c("chr1", "chr1"), ranges = IRanges(start = >> >> >> c(1,5), width = 7)) >> >> >> gr2 = GRanges(seqnames = "chr1", ranges = IRanges(start = 1, end = >> >> >> 4)) >> >> >> pintersect(gr1, rep(gr2, 2)) >> >> >> >> >> >> GRanges with 2 ranges and 0 metadata columns: >> >> >> seqnames ranges strand >> >> >> <rle> <iranges> <rle> >> >> >> [1] chr1 [1, 4] * >> >> >> [2] chr1 [5, 4] * >> >> >> --- >> >> >> seqlengths: >> >> >> chr1 >> >> >> NA >> >> >> >> >> >> The second element in the return GRanges should be empty. I would >> >> >> therefore expect that the return length of the pintersect would have >> >> >> length 1, despite the fact that the first object has length 2. >> >> >> >> >> >> Kasper >> >> >> >> >> >> _______________________________________________ >> >> >> 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 >> >> > >> >> > >> >> >> >> _______________________________________________ >> >> 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 >> > >> > > >