[BioC] Probe matching using vmatchPDict

Ian Henry 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,  
with.indels,  :
   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,


Ian Henry
MPI-CBG Dresden
Pfotenhauerstrasse 108
01307 Dresden

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