On 04/24/2015 11:08 AM, Peter Haverty wrote:
Good catch. We'll want the strand in case we need to go back to a GRanges.
I would make the strand addition optional with the default of FALSE.
It's nice to have a column of strings you can paste right into a genome
browser (sorry Michael :-) ). I often pass my bench collaborators a
spreadsheet with such a column.
as.character(unstrand(gr)) ?
3 reasons I'm not too keen about 'ignore.strand=TRUE' being the default:
(1) Many functions and methods in GenomicRanges/GenomicAlignments
have an 'ignore.strand' argument. For consistency, the default
value has been set to FALSE everywhere. Note that this was done
even if this default doesn't reflect the most common use case
(e.g. summarizeOverlaps).
(2) I think it's good to have the default behavior of as.character()
allow going back and forth between GRanges and character vector
without losing the strand information.
(3) The "table" method for Vector would break if as.character was
ignoring the strand by default. Can be worked-around by
implementing a method for GenomicRanges objects but...
Hope that makes sense.
H.
Pete
____________________
Peter M. Haverty, Ph.D.
Genentech, Inc.
phave...@gene.com <mailto:phave...@gene.com>
On Fri, Apr 24, 2015 at 10:50 AM, Hervé Pagès <hpa...@fredhutch.org
<mailto:hpa...@fredhutch.org>> wrote:
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>
<mailto: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>
<mailto: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>
<mailto:phave...@gene.com <mailto:phave...@gene.com>>
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Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
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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 <mailto:hpa...@fredhutch.org>
Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
--
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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