Repeat masker sequences as GRanges object

Hermann Norpois <[email protected]> Thu, 11 Sep 2014 12:16:59 +0200

Newsgroups	gmane.science.biology.informatics.conductor
Message-ID	<CAKyZeBvqZnEchDZQf3Ceu+4XSDj2JOR5YW6zs3=x7Et0HTJgBA@mail.gmail.com>

Hello,

I would like to have repeat sequences as GRanges object
I started with ...

library (BSgenome.Hsapiens.UCSC.hg19)
ch1 <- Hsapiens$chr1
active (masks (ch1))
AGAPS   AMB    RM   TRF
 TRUE  TRUE FALSE FALSE
active (masks(ch1))["RM"] <- TRUE
active (masks (ch1))
AGAPS   AMB    RM   TRF
 TRUE  TRUE  TRUE FALSE

Can anyboldy give me a hint how to continue.

Thanks
hermann

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