Entering edit mode
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
>
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