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

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, Herv? Pag?s <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

--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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