[Bioc-devel] deprecation of keepSeqlevels and renameSeqlevels
Martin Morgan
mtmorgan at fhcrc.org
Sun May 19 03:00:25 CEST 2013
On 05/18/2013 05:42 PM, Martin Morgan wrote:
> Some of the most common operations are straight-forward, e.g.,
>
> > gr = GRanges(paste0("chr", c(1:22, "X", "Y")), IRanges(1, 100))
> > seqlevels(gr) = sub("chr", "ch", seqlevels(gr))
To get a more comprehensive example I should have followed my own advice and
grabbed from the help page!
## Rename:
seqlevels(txdb) <- sub("chr", "", seqlevels(txdb))
seqlevels(txdb)
seqlevels(txdb) <- paste0("CH", seqlevels(txdb))
seqlevels(txdb)
seqlevels(txdb)[seqlevels(txdb) == "CHM"] <- "M"
seqlevels(txdb)
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