[BioC] xmapcore get intronic sequence
Tim Yates
tyates at picr.man.ac.uk
Thu Jul 29 10:23:06 CEST 2010
Hi Steve,
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"
Tim
On 29/07/2010 09:09, "Steve Taylor" <stephen.taylor at imm.ox.ac.uk> wrote:
> Hi Tim,
>
>> There are a couple of options:
>>
>> 1) Some of your probesets don't hit exons
>> 2) Some of your probesets hit the same exons
>>
...snip...
>> Fingers crossed this gets to the bottom of it ;-)
>
> Some of these are obviously not hitting exons despite having valid probesetids
> (I just double checked they are real probesets by going to the Netaffx site).
> So:
>
>> dim(as.data.frame(probeset.to.exon( probesetids, rm.unreliable=F,
>> as.vector=F)))
> [1] 1666 10
>
> My input list of probesetids was 1771. So there are still some missing :-(.
>
> It seems the only way round this for me is to write a loop and test if
> probeset.to.exon returns anything. How about a rm.notfound=T or F parameter at
> some point in the future (he asked hopefully! :-)).
>
> Thanks,
>
> Steve
>
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