On 12/13/2013 01:49 PM, Michael Lawrence wrote:
Thanks, makes sense. Didn't realize we could dispatch on the 'i'
parameter. I sort of recall the perception that we couldn't, and that
was one of the main motivations behind seqselect. But it does appear
possible.
Well I was hoping I could do this but it doesn't work :-/
Found in the man page for `[`:
S4 methods:
These operators are also implicit S4 generics, but as primitives,
S4 methods will be dispatched only on S4 objects ‘x’.
OK, fair enough. But the following is really misleading:
> library(IRanges)
> `[`
.Primitive("[")
> getGeneric("[")
standardGeneric for "[" defined from package "base"
function (x, i, j, ..., drop = TRUE)
standardGeneric("[", .Primitive("["))
<bytecode: 0x168cba0>
<environment: 0x1ccfd90>
Methods may be defined for arguments: x, i, j, drop
Use showMethods("[") for currently available ones.
So the implicit generic actually does dispatch on 'i'.
I can see my new [,vector,Ranges method:
> selectMethod("[", c("vector", "Ranges"))
Method Definition:
function (x, i, j, ..., drop = TRUE)
{
if (!missing(j) || length(list(...)) > 0L)
stop("invalid subsetting")
extractROWS(x, i)
}
<environment: namespace:IRanges>
Signatures:
x i
target "vector" "Ranges"
defined "vector" "Ranges"
And dispatch works if I explicitly call the generic:
> getGeneric("[")(letters, IRanges(4, 8))
[1] "d" "e" "f" "g" "h"
but not if I call the primitive:
> letters[IRanges(4, 8)]
Error in letters[IRanges(4, 8)] : invalid subscript type 'S4'
Seems like the primitive first checks 'x' and only if it's an
S4 object it then delegates to the implicit S4 generic. Probably
for performance reasons as it avoids the cost of having to perform
full multiple dispatch when 'x' is an ordinary objects.
The following hack works:
> `[` <- getGeneric("[")
> letters[IRanges(4, 8)]
[1] "d" "e" "f" "g" "h"
but putting this in IRanges feels wrong (I tried and it caused
troubles with ref classes).
So I guess I should go ahead and export/document extractROWS()
and replaceROWS(). What are the other options?
In the mean time of course you can always pass your Ranges or Rle
subscript thru unlist() or as.vector() first (not much more typing
than doing seqselect() and I don't expect this will impact performance
too much in practise).
H.
Michael
On Fri, Dec 13, 2013 at 1:10 PM, Hervé Pagès <[email protected]
<mailto:[email protected]>> wrote:
Hi Michael,
On 12/13/2013 01:03 PM, Michael Lawrence wrote:
I used to use seqselect for subsetting ordinary R vectors by
Ranges and
Rle. IRanges:::extractROWS does this, but it's hidden behind the
namespace.
What is the public way of doing this?
Maybe we just need to export extractROWS()? Or something with a
better name?
I'll add [,vector,Ranges and [,vector,Rle methods (and probably also
[,factor,Ranges and [,factor,Rle). They'll just be wrappers to
IRanges:::extractROWS which I'd like to keep hidden.
Was not sure people where doing this on ordinary R vectors so was
waiting for someone to speak up.
H.
Michael
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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: [email protected]
Phone: (206) 667-5791
Fax: (206) 667-1319
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