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

[Michael Lawrence]

Sorry, one more concern, if you're thinking of using as a range key, you
will need the strand, but many use cases might not want the strand on
there. Like for pasting into a genome browser.

On Fri, Apr 24, 2015 at 10:18 AM, Michael Lawrence <michafla at gene.com>
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.
>
>
> 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
>>
>
>

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