While it's cool that seqlevels<- has become so flexible, I still claim that
rename/keep/drop would be a lot easier to read, because they describe the
high-level operation, and there's no reason to deprecate them. They're also
easier to remember. For example, for dropping with seqlevels<-, the user
needs to remember that "force" is necessary to drop. Much easier to just
say "dropSeqlevels(), please". And reimplementing keepSeqlevels is still
too complicated. Is it such a maintenance burden to have these simple
wrappers sit on top of the low-level manipulators?
Another suggestion: renameSeqlevels should not require a named vector (in
cases where it is unnamed, require that it is parallel to the existing
seqlevels, as with seqlevels<-).
Michael
On Sat, May 18, 2013 at 6:00 PM, Martin Morgan <mtmor...@fhcrc.org> wrote:
> 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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