[Bioc-devel] deprecation of keepSeqlevels and renameSeqlevels

Valerie Obenchain vobencha at fhcrc.org
Thu May 30 01:20:47 CEST 2013

Hi all,

keepSeqlevels(), dropSeqlevels(), renameSeqlevels() and the new 
restoreSeqlevels() are in GenomicRanges 1.13.16.

Major changes:

- These are high-level functions that wrap seqlevels(), not generics 
with methods.

- All except restoreSeqlevels accept a named or unnamed character vector.

- restoreSeqlevels is built on the new low-level seqlevels0() and 
currently applies only to TranscriptDb. (We plan to support this for 
BSgenome and SNPLocs as well.) The issue is that when seqlevels are 
changed directly on the TranscriptDb (reference class) it is difficult 
for the user to get back to the original names if they want them. Simply 
reloading the package doesn't do it. There is an example of this on the 
man page. The seqlevels0,TranscriptDb-method is in GenomicFeatures 1.13.11.

Let me know if you have problems / questions.


On 05/18/2013 05:18 PM, Michael Lawrence 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
> 	[[alternative HTML version deleted]]
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