[Bioc-devel] as.character method for GenomicRanges?

It would be nice to have a single function call that would hide these
details. It could probably be made more efficient also by avoiding
multiple matching, unnecessary revmap lists, etc. tableAsGRanges() is
not a good name but it conveys what I mean (does that make it actually
good?).

On Mon, Apr 27, 2015 at 12:23 PM, Herv? Pag?s <hpages at fredhutch.org
<mailto:hpages at fredhutch.org>> wrote:

    On 04/24/2015 11:41 AM, Michael Lawrence wrote:

        Taking this a bit off topic but it would be nice if we could get the
        GRanges equivalent of as.data.frame(table(x)), i.e., unique(x)
        with a
        count mcol. Should be easy to support but what should the API be
        like?


    This was actually the motivating use case for introducing
    findMatches/countMatches a couple of years ago:

       ux <- unique(x)
       mcols(ux)$Freq <- countMatches(ux, x)

    Don't know what a good API would be to make this even more
    straightforward though. Maybe via some extra argument to unique()
    e.g. 'with.freq'? This is kind of similar to the 'with.revmap'
    argument of reduce(). Note that unique() could also support the
    'with.revmap' arg. Once it does, the 'with.freq' arg can also
    be implemented by just calling elementLengths() on the "revmap"
    metadata column.

    H.


        On Fri, Apr 24, 2015 at 10:54 AM, Herv? Pag?s
        <hpages at fredhutch.org <mailto:hpages at fredhutch.org>
        <mailto:hpages at fredhutch.org <mailto:hpages at fredhutch.org>>> wrote:

             On 04/24/2015 10:18 AM, Michael Lawrence wrote:

                 It is a great idea, but I'm not sure I would use it to
        implement
                 table(). Allocating those strings will be costly. Don't we
                 already have
                 the 4-way int hash? Of course, my intuition might be
        completely
                 off here.


             It does use the 4-way int hash internally. as.character()
        is only used
             at the very-end to stick the names on the returned table
        object.

             H.



                 On Fri, Apr 24, 2015 at 9:59 AM, Herv? Pag?s
                 <hpages at fredhutch.org <mailto:hpages at fredhutch.org>
        <mailto:hpages at fredhutch.org <mailto:hpages at fredhutch.org>>
                 <mailto:hpages at fredhutch.org
        <mailto:hpages at fredhutch.org> <mailto:hpages at fredhutch.org
        <mailto:hpages at fredhutch.org>>>> wrote:

                      Hi Pete,

                      Excellent idea. That will make things like table()
        work
                 out-of-the-box
                      on GenomicRanges objects. I'll add that.

                      Thanks,
                      H.



                      On 04/24/2015 09:43 AM, Peter Haverty wrote:

                          Would people be interested in having this:

                          setMethod("as.character", "GenomicRanges",
                                      function(x) {
                                          paste0(seqnames(x), ":",
        start(x), "-",
                 end(x))
                                      })

                          ?

                          I find myself doing that a lot to make unique
        names or for
                          output that
                          goes to collaborators.  I suppose we might
        want to tack
                 on the
                          strand if it
                          isn't "*".  I have some code for going the other
                 direction too,
                          if there is
                          interest.



                          Pete