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

[Hervé Pagès]

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, Hervé Pagès <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, Hervé Pagès
>         <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
>
>                  ____________________
>                  Peter M. Haverty, Ph.D.
>                  Genentech, Inc.
>         phaverty at gene.com <mailto:phaverty at gene.com>
>         <mailto:phaverty at gene.com <mailto:phaverty at gene.com>>
>
>                           [[alternative HTML version deleted]]
>
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>
>              --
>              Hervé Pagès
>
>              Program in Computational Biology
>              Division of Public Health Sciences
>              Fred Hutchinson Cancer Research Center
>              1100 Fairview Ave. N, M1-B514
>              P.O. Box 19024
>              Seattle, WA 98109-1024
>
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>
>     --
>     Hervé Pagès
>
>     Program in Computational Biology
>     Division of Public Health Sciences
>     Fred Hutchinson Cancer Research Center
>     1100 Fairview Ave. N, M1-B514
>     P.O. Box 19024
>     Seattle, WA 98109-1024
>
>     E-mail: hpages at fredhutch.org <mailto:hpages at fredhutch.org>
>     Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
>     Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>
>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319