[BioC] xmapcore get intronic sequence

[Tim Yates]

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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