[BioC] transcriptLocs2refLocs Bug when strand is negative

[Cook, Malcolm]

Martin,

Again, thanks for your time to educate.  All is clear.  The problem was
mine.

--Malcolm


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
>> https://stat.ethz.ch/pipermail/bioconductor/2011-March/038173.html
>>
>> I think you will agree that the third result should be:
>> [[3]]
>> [1] 5899 6291
>
>Hi Malcolm
>
>In the example the exon coordinates (always in 1-based 'leftmost'
>cooredinates') are
>
>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.
>
>Martin
>
>>
>> As a workaround, I have implemented a version in R using a new generic,
>> named `at`
>>
>> https://gist.github.com/3560692
>>
>>
>> I would be happy to receive confirmation that this is a bug, and
>>comments
>> from anyone on the approach to the workaround I have adopted, especially
>> as regards performance comparison with
>>
>> Thanks,
>>
>> Malcolm Cook
>> Stowers Institute for Medical Research
>>
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>
>
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