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

[Michael Lawrence]

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?

On Fri, Apr 24, 2015 at 10:54 AM, Hervé Pagès <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>> 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>
>>
>>                  [[alternative HTML version deleted]]
>>
>>         _______________________________________________
>>         Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>
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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>
>>
>>
>>     _______________________________________________
>>     Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org> mailing
>> list
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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
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

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