On Wed, May 13, 2009 at 7:05 AM, Nicolas Delhomme <[email protected]> wrote:
> Hi all,
>
> I've got the impression that the as.matrix method of the RangesMatchingList
> does not work as it should.
>
> I have a RangesMatchingList which I obtained by using the overlap (from the
> RangesList class) function that takes two RangesList as input. When I apply
> as.matrix() on the RangesMatchingList, it gives me the following error:
>
> Error in .Method(..., deparse.level = deparse.level) :
> number of rows of matrices must match (see arg 2)
>
> The function is pretty easy:
>
> setMethod("as.matrix", "RangesMatchingList", function(x) {
> cbind(space = space(x), do.call(cbind, lapply(x, as.matrix)))
> })
>
> When I replace the cbind in the do.call by an rbind, it's already better
>
Thanks, yes this was a bug. As the documentation states, RangesMatchingList
was considered experimental and not something that was really tested. But I
should have done a better job.
> Warning message:
> In .Method(..., deparse.level = deparse.level) :
> number of rows of result is not a multiple of vector length (arg 1)
>
> This is due to the fact that space(x) returns many more spaces than there
> are overlaps.
>
This is a bug in space().
>
> I could solve that by changing the function into:
>
> setMethod("as.matrix", "RangesMatchingList", function(x) {
> do.call(rbind,lapply(c(1:length(x)),function(i){mat <-
> as.matrix(x[[i]]);cbind(space=rep(names(x)[[i]],nrow(mat)),mat)}))
> })
>
> Now, I do not know if I might have a particular use-case (having a
> RangesMatchingList coming from the RangesList overlap function) that you
> guys did not think of.
>
It turns out that I had to rethink this method. As above, the user will
receive a character matrix, which probably isn't very useful. Could
translate the space names into integer IDs, but in order to use that, one
would have to split the matrix and loop over each block. In that case, it
would just be easier to loop over the RangesMatchingList. Thus, I changed
the function to return a doublet matrix, just like RangesMatching, where the
indices are adjusted so that they are aligned with the result of calling
'unlist' on the subject and query RangesLists (ie the index is global). I
think this will satisfy more use cases, but I'm not sure.
These changes were applied in both trunk and release.
Thanks for the feedback, and I'd appreciate more if you have any,
Michael
>
> Just let me know,
>
> Best,
>
> ---------------------------------------------------------------
> Nicolas Delhomme
>
> High Throughput Functional Genomics Center
>
> European Molecular Biology Laboratory
>
> Tel: +49 6221 387 8426
> Email: [email protected]
> Meyerhofstrasse 1 - Postfach 10.2209
> 69102 Heidelberg, Germany
>
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