[BioC] using a gtf file to map reads

[Valerie Obenchain]

Great. I'll go ahead and put this in GenomicFeatures with credit to you 
and Alejandro.

Thanks.
Valerie

On 06/11/2013 09:39 AM, Michael Love wrote:
> hi Valerie,
>
> On Tue, Jun 11, 2013 at 6:13 PM, Valerie Obenchain <vobencha at fhcrc.org> wrote:
>> Hi Mike (Love),
>>
>> Would you be interested in contributing a disjointExons() to
>> GenomicFeatures? I think this extraction would be useful to many. Maybe we
>> also want a disjointExonsBy() but the only 'by' would be genes ...?
>>
>> Valerie
>>
>
> I'd be happy to contribute any of this code in parathyroidSE.
> Alejandro Reyes has formalized this part of the code into the
> following function in DEXSeq >= 1.6.0:
>
>> prepareAnnotationForDEXSeq
> function (transcriptDb, aggregateGenes = FALSE, includeTranscripts = TRUE)
> {
>      stopifnot(is(transcriptDb, "TranscriptDb"))
>      exonsByGene <- exonsBy(transcriptDb, by = "gene")
>      exonicParts <- disjoin(unlist(exonsByGene))
>      if (!aggregateGenes) {
>          overlaps <- findOverlaps(exonicParts, exonsByGene)
>          geneNames <- names(exonsByGene)[subjectHits(overlaps)]
> .....
>
> best,
>
> Mike
>