A tangential remark, nevertheless...:
seq(along=x)
is equivalent to and sometimes probably closer to what you want than
c(1:length(x))
Best wishes
Wolfgang
Nicolas Delhomme ha scritto:
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
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.
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.
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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--
Best wishes
Wolfgang
------------------------------------------------
Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber
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