[BioC] Repeat masker sequences as GRanges object

Hermann Norpois hnorpois at gmail.com
Thu Sep 11 12:16:59 CEST 2014


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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