[BioC] Extract masked sequences

Mercier Eloi Eloi.Mercier at ircm.qc.ca
Thu Jan 14 21:22:06 CET 2010


I wondering if anybody can hep me to generate masked (by RepeatMasker for instance) sequences.

I'm currently using Bsgenome to extract sequence from a BED file such as :
FastaSeq<-getSeq(genome,"chr1",start=1000,end=1200, as.character=FALSE)

I know that Bsgenome contains masks that can be apply by using :
chr1 <- genome$chr1
active(masks(chr1)) <- TRUE

So, I'm trying to use it to change the masks of the genome object. But I cannot modify it :
 active(masks(genome$chr1)) <- TRUE
Error in `$<-`(`*tmp*`, "chr1", value = <S4 object of class "MaskedDNAString">) :
  no method for assigning subsets of this S4 class

Is there a way get the masked sequence with the getSeq function ?


Eloi Mercier
Computational Biology, IRCM
110 av. Des Pins O.
Canada, QC

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