[BioC] Probe matching using vmatchPDict

Hervé Pagès hpages at fhcrc.org
Mon Jul 25 19:57:04 CEST 2011

Hi Ian,

On 11-07-25 08:41 AM, Ian Henry wrote:
> Hello,
> I'm trying to match a list of 60mer probes against a transcriptome to
> see which probes hit which transcripts.
> I have my 60mer probe list as a DNAStringSet and also as a "PDict"
>  > probeset <- DNAStringSet(probelist$ProbeSeq)
>  > probeset_pdict <- PDict(probeset)
> My transcriptome was created as follows:
>  > zv9txdb <- makeTranscriptDbFromUCSC(genome = "danRer7", tablename =
> "ensGene")
>  > zv9_tx <- extractTranscriptsFromGenome(Drerio, zv9txdb)
> To find which transcripts are hit by the probes I've used vwhichPDict:
>  > tx_matches <- vwhichPDict(probeset_pdict, zv9_tx)
> which works brilliantly!
> However, I also would like the locations of the matches and so tried:
>  > tx_locs <- vmatchPDict(probeset_pdict, zv9_tx)
> This doesn't work and errors to say:
> Error in .local(pdict, subject, max.mismatch, min.mismatch, with.indels, :
> vmatchPDict() is not ready yet, sorry
> Does this just mean it's not yet implemented and is there a
> solution/workaround?

It is not yet implemented and has been on my TODO list for a long time,

One workaround I can think of: use matchPDict in a loop (you loop over
the transcripts). The Drerio transcriptome is not be that big so it
might run in descent time. It might help a little bit to reduce the
size of the problem by getting rid of the probes and transcripts that
don't have hit (based on the result of vwhichPDict).

Let me know if that's not fast enough or if you need further help with


> vmatchPDict(probeset_pdict, Drerio) works but I'd really like to match
> to the transcriptome rather than the genome.
> Thanks for any advice in advance,
> Ian
> Ian Henry
> MPI-CBG Dresden
> Pfotenhauerstrasse 108
> 01307 Dresden
> Germany
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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P.O. Box 19024
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