Arnaud,
The BSgenome object, in this case Hsapiens, contains references to on
disk storage of information such as masks. Since this information is not
in memory and the data stored on disk is considered read-only, you
cannot change the mask information on a BSgenome object. Instead, you
need to modify the masks chromosome by chromosome after they have been
loaded into memory as you showed in your code below.
What is your use case that motivated your e-mail?
If you never want to deal with masks, you can always use the unmasked
function to strip the masks when you load the chromosome:
> unmasked(Hsapiens$chr1)
247249719-letter "DNAString" instance
seq:
TAACCCTAACCCTAACCCTAACCCTAACCCTAACCC...NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
Patrick
Droit Arnaud wrote:
Hi,
I wondering if anybody can help me to generate masked (by RepeatMasker for
instance) sequences.
I'm currently using Bsgenome to extract sequence from a BED file such as :
library(BSgenome.Hsapiens.UCSC.hg18)
genome<-Hsapiens
FastaSeq<-getSeq(genome,"chr1",start=1000,end=1200, as.character=FALSE)
I know that Bsgenome contains masks that can be apply by using :
chr1 <- genome$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 ?
Thanks.
Arnaud.
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