[Bioc-devel] equivalent of seqselect,vector,Rle

[Hervé Pagès]

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 <hpages at fhcrc.org
> <mailto:hpages at 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]]
>
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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: hpages at fhcrc.org <mailto:hpages at 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: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319