On 04/24/2015 10:21 AM, Michael Lawrence wrote:
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.
What about appending the strand only for GRanges objects that
have at least one range that is not on *?
setMethod("as.character", "GenomicRanges",
function(x)
{
if (length(x) == 0L)
return(character(0))
ans <- paste0(seqnames(x), ":", start(x), "-", end(x))
if (any(strand(x) != "*"))
ans <- paste0(ans, ":", strand(x))
ans
}
)
> as.character(gr)
[1] "chr1:1-10" "chr2:2-10" "chr2:3-10" "chr2:4-10" "chr1:5-10"
[6] "chr1:6-10" "chr3:7-10" "chr3:8-10" "chr3:9-10" "chr3:10-10"
> strand(gr)[2:3] <- c("-", "+")
> as.character(gr)
[1] "chr1:1-10:*" "chr2:2-10:-" "chr2:3-10:+" "chr2:4-10:*"
"chr1:5-10:*"
[6] "chr1:6-10:*" "chr3:7-10:*" "chr3:8-10:*" "chr3:9-10:*"
"chr3:10-10:*"
H.
On Fri, Apr 24, 2015 at 10:18 AM, Michael Lawrence <micha...@gene.com
<mailto:micha...@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 <hpa...@fredhutch.org
<mailto:hpa...@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.
phave...@gene.com <mailto:phave...@gene.com>
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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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E-mail: hpa...@fredhutch.org <mailto:hpa...@fredhutch.org>
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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: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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