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

[Hervé Pagès]

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]]
>
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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
Phone:  (206) 667-5791
Fax:    (206) 667-1319