[BioC] xmapcore get intronic sequence

[Steve Taylor]

Hi Tim,

> Yeah, looks like they are missing exons.  I'll have a think about the
> rm.notfound idea, but that would require the method to return two things;
> the list of exons, and a list of probesets which didn't hit. If as.vector=F
> is passed, it would again require two results, or a RangedData object with
> some rows with missing IRanges objects (which I don't think is possible --
> and would break the rest of xmapcore even if it were)
> I think for now, a loops is the only way
>
> Or it should be possible to write a method that filters your list of
> probeset ids, removing the ones which appear in the IN1 column of the
> RangedData object.  Something like:
>
>> probesetIds = c( '3081222', 'doesntexist', '3081223' )
>> exons = probeset.to.exon( probesetIds, as.vector=F )
>
> Then, to get the list of probesets that didn't match to anything:
>
>> probesetIds[ !( probesetIds %in% exons[[ 'IN1' ]] ) ]
> [1] "doesntexist"
>

That's a good solution.

Thanks for your help,

Steve