Hi Patrick Thanks for the quick response + fix. I just d/l'd + installed the package from svn, and it looks good. Cheers, -steve On Aug 18, 2009, at 1:23 PM, Patrick Aboyoun wrote: > Thanks Steve, > You did indeed find a bug, which turned out to be in the gaps method > for IRanges objects. Back on August 6th, I fixed the corner case > > gaps(IRanges()) > > and inadvertently broke the corner case > > gaps(IRanges(), start = <<int>>, end = <<int>>) > > I just check in a fix to svn (IRanges version 1.3.55) that corrects > this issue. > > > suppressMessages(library(IRanges)) > > i1 <- IRanges(start=c(1, 10, 20), width=10) > > intersect(i1, i1) > IRanges instance: > start end width > [1] 1 29 29 > > sessionInfo() > R version 2.10.0 Under development (unstable) (2009-08-05 r49073) > i386-apple-darwin9.7.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1] IRanges_1.3.55 > > > > Patrick > > > Steve Lianoglou wrote: >> Hi, >> >> [I'm using R 2.10-devel w/ latest IRanges (version info below)] >> >> I'm a bit confused to the behavior of intersect. Namely, the >> intersection with *some* IRanges object with itself returns a 0-row >> range, but I feel like it should return itself (no matter what). >> >> Some examples: >> >> 1. if the IRange "elements" represent a contiguous range, the >> `intersect`-ion with itself is empty, but its `pintersect`-ion isn't: >> >> R> i1 <- IRanges(start=c(1, 10, 20), width=10) >> R> intersect(i1,i1) >> IRanges instance: >> [1] start end width >> <0 rows> (or 0-length row.names) >> >> R> pintersect(i1,i1) >> IRanges instance: >> start end width >> [1] 1 10 10 >> [2] 10 19 10 >> [3] 20 29 10 >> >> 2. If the IRanges "elements" represent some disjoint range, both >> intersect and pintersect run as expected (to me): >> >> R> i2 <- IRanges(start=c(1,10,20), width=8) >> R> i2 >> IRanges instance: >> start end width >> [1] 1 8 8 >> [2] 10 17 8 >> [3] 20 27 8 >> >> R> pintersect(i2,i2) >> IRanges instance: >> start end width >> [1] 1 8 8 >> [2] 10 17 8 >> [3] 20 27 8 >> >> Is this the expected behavior? Or is the first example in (1) a bug? >> >> Thanks, >> -steve >> >> R> > sessionInfo() >> R version 2.10.0 Under development (unstable) (2009-08-01 r49053) >> i386-apple-darwin9.7.0 >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] ShortRead_1.3.25 lattice_0.17-25 BSgenome_1.13.10 >> Biostrings_2.13.32 IRanges_1.3.53 doMC_1.1.1 >> multicore_0.1-3 >> [8] foreach_1.2.1 codetools_0.2-2 iterators_1.0.2 >> ARE.utils_0.1.0 >> >> loaded via a namespace (and not attached): >> [1] Biobase_2.5.5 grid_2.10.0 hwriter_1.1 tools_2.10.0 >> >> -- >> Steve Lianoglou >> Graduate Student: Computational Systems Biology >> | Memorial Sloan-Kettering Cancer Center >> | Weill Medical College of Cornell University >> Contact Info: http://cbio.mskcc.org/~lianos/contact >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact