[BioC] Probe matching using vmatchPDict
henry at mpi-cbg.de
Mon Jul 25 17:41:46 CEST 2011
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 =
> 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,
vmatchPDict() is not ready yet, sorry
Does this just mean it's not yet implemented and is there a solution/
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,
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