Thanks Patrick! Patrick Aboyoun wrote: > Cei, > I checked in a patch to BioC 2.6 (GenomicRanges 1.0.6) and BioC 2.7 > (GenomicRanges 1.1.16) that fixes the issue you found in the intersect > and setdiff methods for GRanges objects when the two objects don't have > the same sequence names. These new packages will be available on > bioconductor.org within the next 36 hours. > > The intersect and setdiff method for GRanges now form the union of > sequence names for both objects before performing their operations. The > output for the examples you sent are now > > > library(GenomicRanges) > > gr1 <- GRanges(seqnames = c("chr1", "chr2", "chr3", "chr4"), > + ranges = IRanges(1:4, width = 10), > + strand = c("-", "+", "+", "+")) > > gr2 <- GRanges(seqnames = c("chr1", "chr2", "chr5", "chr6"), > + ranges = IRanges(1:4, width = 10), > + strand = c("-", "+", "+", "+")) > > > intersect(gr1,gr2) > GRanges with 2 ranges and 0 elementMetadata values > seqnames ranges strand | > <rle> <iranges> <rle> | > [1] chr1 [1, 10] - | > [2] chr2 [2, 11] + | > > seqlengths > chr1 chr2 chr3 chr4 chr5 chr6 > NA NA NA NA NA NA > > > setdiff(gr1,gr2) > GRanges with 2 ranges and 0 elementMetadata values > seqnames ranges strand | > <rle> <iranges> <rle> | > [1] chr3 [3, 12] + | > [2] chr4 [4, 13] + | > > seqlengths > chr1 chr2 chr3 chr4 chr5 chr6 > NA NA NA NA NA NA > > > sessionInfo() > R version 2.12.0 Under development (unstable) (2010-07-01 r52425) > Platform: i386-apple-darwin9.8.0/i386 (32-bit) > > 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] GenomicRanges_1.1.16 IRanges_1.7.10 > > > Cheers, > Patrick > > > > On 7/8/10 4:55 PM, Patrick Aboyoun wrote: >> Cei, >> Thanks for the bug report. I am looking into the issue now and will >> have a patch out shortly. >> >> >> Cheers, >> Patrick >> >> >> On 7/8/10 9:22 AM, Cei Abreu-Goodger wrote: >>> Hello all, >>> >>> When you have two GRanges objects which don't have the same seqnames >>> factor, you can get very unexpected behavior. >>> >>> Would it be possible to get an error/warning when this is attempted? >>> I don't know how many functions are affected, perhaps the functions >>> mentioned below can be modified to produce a more obvious result... >>> >>> Many thanks, >>> >>> Cei >>> >>> >>> Code example / sessionInfo: >>> >>> library(GenomicRanges) >>> gr1 <- GRanges(seqnames = c("chr1", "chr2", "chr3", "chr4"), >>> ranges = IRanges(1:4, width = 10), >>> strand = c("-", "+", "+", "+")) >>> gr2 <- GRanges(seqnames = c("chr1", "chr2", "chr5", "chr6"), >>> ranges = IRanges(1:4, width = 10), >>> strand = c("-", "+", "+", "+")) >>> >>> union(gr1,gr2) >>> # gives expected result, all 6 ranges >>> >>> intersect(gr1,gr2) >>> # includes ranges from the missing gr2 chromosomes >>> >>> setdiff(gr1,gr2) >>> # includes 3 copies of the ranges from the missing gr2 chromosomes >>> >>> >>> sessionInfo() >>> R version 2.11.0 (2010-04-22) >>> i386-apple-darwin9.8.0 >>> >>> locale: >>> [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 >>> >>> attached base packages: >>> [1] stats graphics grDevices datasets utils methods base >>> >>> other attached packages: >>> [1] GenomicRanges_1.0.5 IRanges_1.6.8 Biobase_2.8.0 >>> >>> loaded via a namespace (and not attached): >>> [1] tools_2.11.0 >>> >>> _______________________________________________ >>> 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 >> >> _______________________________________________ >> 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