[BioC] transcriptLocs2refLocs Bug when strand is negative
MEC at stowers.org
Tue Sep 4 18:15:23 CEST 2012
Again, thanks for your time to educate. All is clear. The problem was
On 9/1/12 8:49 AM, "Martin Morgan" <mtmorgan at fhcrc.org> wrote:
>On 08/31/2012 04:22 PM, Cook, Malcolm wrote:
>> Herve et al,
>> I believe that transcriptLocs2refLocs is implemented incorrectly for
>> negative strands.
>> The bug appears in the example of its use you provided in
>> I think you will agree that the third result should be:
>>  5899 6291
>In the example the exon coordinates (always in 1-based 'leftmost'
>start: c(6291L, 5278L)
> end: c(6500L, 5899L)
>so on the minus strand the 5' -> 3' transcript is from 6500 --> 6291 and
>then 5899 -> 5271, and is 832 nt long.
>The first (5') nucleotide on the transcript comes from position 6500,
>the 832nd nucleotide comes from the 3' ('leftmost', when the exon is on
>the minus strand) end of the second exon, at genomic coordinate 5278.
>These are the values that transcriptLocs2refLocs returns.
>> As a workaround, I have implemented a version in R using a new generic,
>> named `at`
>> I would be happy to receive confirmation that this is a bug, and
>> from anyone on the approach to the workaround I have adopted, especially
>> as regards performance comparison with
>> Malcolm Cook
>> Stowers Institute for Medical Research
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> Search the archives:
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