[Bioc-devel] deprecation of keepSeqlevels and renameSeqlevels

[Martin Morgan]

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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