[Bioc-sig-seq] Extract masked sequences

Droit Arnaud Arnaud.Droit at ircm.qc.ca
Fri Jan 15 22:07:08 CET 2010


I wondering if anybody can help 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 ?



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