[Bioc-devel] deprecation of keepSeqlevels and renameSeqlevels
Hi Michael --
On 5/20/2013 5:56 AM, Michael Lawrence wrote:
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<-).
I didn't really indicate what drove my desire to see keepSeqlevels deprecated.
keepSeqlevels, seqlevels<-, and isActiveSeq were developed more or less
independently, and have different contracts. The different contracts are
confusing to the user, as is creating a usable help system when there are
multiple end points for what is a common operation. The help pages of each were
inadequate in different ways. And because the code was developed independently,
support for different objects was inconsistent. So actually, yes, the
maintenance (and use) burden for the previous state of affairs was substantial.
On the other hand, I agree that keepSeqlevels is convenient as a simple wrapper
around seqlevels<-, in the same way that setNames and names<- are both useful.
So we could iterate to
keepSeqlevels <-
function(x, value, ...)
{
seqlevels(x, force=TRUE) <- value
x
}
but I'd be less enthusiastic about maintaining the original contract of
keepSeqlevels, where keepSeqlevels(gr1, gr2), would have worked for two GRanges
objects.
Martin
Michael
On Sat, May 18, 2013 at 6:00 PM, Martin Morgan <mtmorgan at fhcrc.org
<mailto:mtmorgan at 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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