For the second time today, I find myself fully supporting Michael's
suggestion.
On Sat, May 18, 2013 at 8:18 PM, Michael Lawrence <lawrence.mich...@gene.com
> wrote:
> Hi guys,
>
> Just wondering about the rationale of deprecating keepSeqlevels and
> renameSeqlevels. Sure, it's possible to do those things with seqlevels,
> somehow, but those functions make the high-level operation fairly obvious.
> They're very well named, and correspond to typical operations. I don't
> think we should deprecate functions just because they are simple wrappers
> on top of lower level functions. I might even suggest adding a
> dropSeqlevels(), e.g. dropSeqlevels("chrM").
>
> As I understand it, instead of:
> keepSeqlevels(x, "chr1")
>
> We need to do something like:
> seqlevels(x, new2old = 1, force = TRUE) <- "chr1"
> But to be more careful it would be:
> seqlevels(x, new2old = match("chr1", seqlevels(x)), force = TRUE) <- "chr1"
>
> This seqlevels stuff is already confusing to people and the above lines are
> regular visitors on my office white-board. These changes will probably
> cause me to sacrifice yet more of my white-board.
>
> In the future, perhaps we should propose these deprecations on the mailing
> list for discussion, before any code changes.
>
> Michael
>
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>
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