Hello Everyone:
I'm hoping to get some suggestions on this problem i'm having with
subsetting on an R object i've created. I would really appreciate any
advice.
I've created this simple S3 class:
>str(ans)
Class 'myObj' atomic [1:45000] 0.0428 0.0423 0.0554 0.0338 0.0345 ...
..- attr(*, "Size")= int 10
..- attr(*, "Region")= chr "EXON"
I create instances of this class by doing something like this:
ans <- structure(x,class="myObj", Size=length(i),
Region=attr(x,"UTR"))
where x is a vector of reals.
When I subset it via ans[c(2,3,4),c(2,4,8)] I get the result I want (my
subsetting works as if its a two dimensional object for reasons I'll omit
since I don't think its pertinent to the problem).
I've written my subsetting code in C, so my R function is basically just a
wrapper function to a .Call.
"[.myObj" <- function(x, i=NA, j=NA, ...){
.. do some parameter checking...
.. then pass the data on to my C routine...
ans <- .Call("foo",as.numeric(x),as.integer(i),as.integer(j))
ans <- structure(ans,class="myObj", Size=length(i),
Region=attr(x,"UTR"))
return(ans)
}
One of my main goals is to do this subsetting quickly (which is why i do
the subsetting in C) However, when I look at my results returned from
summaryRprof I see these 3 lines that are troubling:
$by.total
total.time total.pct self.time self.pct
"[" 41.54 50.3 0.22 0.3
"[.myObj" 41.32 50.0 0.32 0.4
"as.numeric" 38.58 46.7 38.58 46.7
these times are much much longer than they should be. I'm not sure why
"["
is called twice.
I'm guessing that its being called once for the myObj class, and once for
the underlying atomic structure of a vector of reals.
I've been looking at this issue for a while and trying to mimic other
subsetting packages but with no luck. I think the solution involves
understanding NextMethod("[") but then again I'm not so sure.
Again, I really appreciate any comments or advice!
Thanks a bunch,
Greg W.
