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

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, Herv? Pag?s <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

--
Herv? Pag?s

Program in Computational Biology
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