[Bioc-devel] deprecation of keepSeqlevels and renameSeqlevels

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.michael at 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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