Coercion might suffice. I do remember Patrick optimizing these selections
with e.g. memcpy(), so they are pretty fast. No profiling data though. I do
have some performance critical code that has relied on the Rle-based
extraction. Would be nice to avoid re-evaluating the performance.
On Fri, Dec 13, 2013 at 6:19 PM, Hervé Pagès <hpa...@fhcrc.org> wrote:
> 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 <hpa...@fhcrc.org
>> <mailto:hpa...@fhcrc.org>> 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
>>
>> [[alternative HTML version deleted]]
>>
>> _________________________________________________
>> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org>
>> mailing list
>> https://stat.ethz.ch/mailman/__listinfo/bioc-devel
>>
>> <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
>>
>>
>> --
>> 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...@fhcrc.org <mailto:hpa...@fhcrc.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...@fhcrc.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
>
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