[Bioc-devel] deprecation of keepSeqlevels and renameSeqlevels

On Mon, May 20, 2013 at 4:13 PM, Herv? Pag?s <hpages at fhcrc.org
<mailto:hpages at fhcrc.org>> wrote:

    Hi,


    On 05/20/2013 03:15 PM, Michael Lawrence wrote:

        On Mon, May 20, 2013 at 3:11 PM, Martin Morgan
        <mtmorgan at fhcrc.org <mailto:mtmorgan at fhcrc.org>> wrote:

            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.


    Why would this be called keepSeqlevels() if, depending on how it's used,
    it will either add, drop, rename, or permute the seqlevels?
    Couldn't this be called setSeqlevels?


I thought that new2old was necessary for permuting.

You're right that
adding should be disallowed for keepSeqlevels(). Adding seqlevels is not
a common operation. The two common operations are:
* Permuting, usually because the data were imported in non-canonical
order (seqnameStyle was designed to address this, no?).

* Subsetting, either by keeping or dropping.

Two main reasons: taking a
small slice of the data for prototyping, or removing problematic
chromosomes (sex, circular). This goes back to bsapply and the exclude
argument.

Michael


    H.



        Well, I wasn't even aware of that feature, so you've made your
        point about
        the documentation ;) Sounds like a good compromise to me.

        Thanks for understanding,
        Michael



            Martin


                Michael






                On Sat, May 18, 2013 at 6:00 PM, Martin Morgan
                <mtmorgan at fhcrc.org <mailto:mtmorgan at fhcrc.org>
                <mailto: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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                Research Center
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            --
            Dr. Martin Morgan, PhD

            Fred Hutchinson Cancer Research Center
            1100 Fairview Ave. N.
            PO Box 19024 Seattle, WA 98109


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