Hi Michael,
Thanks a lot. This is working very nicely. However, the user has to
pay attention to the fact that it's query and subject are ordered in
the same way to properly use the index generated.
For example, my subject has the names: "2L" "2R" "3L" "3R" "4" "X"
and the query: "4" "X" "3R" "2R" "2L" "3L". The overlap function
takes care of this and compare the right spaces. It returns a
RangesMatchingList with names:
"4" "X" "3R" "2R" "2L" "3L". This means that when I export the
result as a matrix, the indices will be corrupted.
I can think of two solutions:
Either, there should be a warning emitted (when doing the overlap if
the names are not ordered the same)
Or, and that would be my preferred solution, have an additional slot
in the RangesMatchingList holding the mapping index from the query
names to the subject names. This could then be used by the as.matrix
method to return the "correct" indices. This should make it safe for
the case where the user does not provide a query and a subject ordered
in the same way. And it should be robust to the cases where the query
and subject spaces are not entirely identical.
Well, this is just my two cents' worth as I'm not (yet) so familiar
with the code.
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
---------------------------------------------------------------
On 13 May 2009, at 22:20, Michael Lawrence wrote:
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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