Hi, I just checked in a change that should preserve order. I don't have any great test cases though, so please let me know if it's working for you. Thanks, Michael On Wed, Aug 24, 2011 at 8:28 AM, Andrew Jaffe <ajaffe@jhsph.edu> wrote: > I'm having a problem maintaining the ordering of my GRanges object > when I lift it over using rtracklayer::liftOver. For example: > > > g # my regions > GRanges with 5 ranges and 0 elementMetadata values > seqnames ranges strand | > <rle> <iranges> <rle> | > [1] chr19 [ 13130686, 13133039] * | > [2] chr4 [160026138, 160028079] * | > [3] chr12 [ 65671230, 65672140] * | > [4] chr8 [ 19615409, 19616461] * | > [5] chr14 [ 99706752, 99708661] * | > > > chain = import.chain("hg19ToHg18.over.chain") # from UCSC > > lifted = liftOver(g, chain) # suppressed unmatched chrs > > lifted > GRanges with 5 ranges and 0 elementMetadata values > seqnames ranges strand | > <rle> <iranges> <rle> | > [1] chr4 [160245588, 160247529] * | > [2] chr8 [ 19659689, 19660741] * | > [3] chr12 [ 63957497, 63958407] * | > [4] chr14 [ 98776505, 98778414] * | > [5] chr19 [ 12991686, 12994039] * | > > This is just a toy example with 5 regions all on different > chromosomes, but with real data where there are multiple regions per > chromosome, I am unable to determine the resulting matched lifted data > for a particular region. Is there any way to preserve the ordering of > my original list in the liftOver output? Presorting by chromosome and > position might work 99% of time, but the ordering of some regions > might shift during the liftOver, and I would not be able to tell if > this occurred. > > Thanks a lot, > Andrew Jaffe > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]