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

[Michael Lawrence]

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.


On Fri, Apr 24, 2015 at 9:59 AM, Hervé Pagès <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
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
> --
> 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
>
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

	[[alternative HTML version deleted]]