Hi Pete -- looks like a good idea.
I think the generic could be adjusted to pass named (not x, y) args to methods,
rather than trying (incorrectly) to combine them. I don't think the
inefficiency of recursion is a particular concern, because it is not like
hundreds (or even tens) of objects are typically being combined.
combine() takes the approach of implementing methods for each component -- so I
guess DataFrame, GRanges, GRangesList, SimpleList (for the assays, which are
matrix, which are already combine()-able).
Any interest in re-implementing your code along these lines (as methods on the
building blocks)? Some guidance might come from selectMethod("combine",
c("data.frame", "data.frame")).
FWIW --
stop(paste0()) is just stop(), which accepts multiple arguments and pastes them
together without a separator.
x@NAMES is names(), as in names(GRanges("chr1", IRanges(1, 10, names="A")))
?elementMetadata says "Alternatives to 'mcols' functions. Their [i.e.,
elementMetadata] use is discouraged."
> -----Original Message-----
> From: Bioc-devel [mailto:[email protected]] On Behalf Of
> Peter Hickey
> Sent: Wednesday, October 14, 2015 9:52 PM
> To: [email protected]
> Subject: [Bioc-devel] A method for combining SummarizedExperiment
> objects
>
> I often find myself with multiple `SE` objects (I'm using `SE` as a shorthand
> for
> the `SummarizedExperiment0` and `RangedSummarizedExeriment` classes),
> each with different samples but possibly non-overlapping features/ranges.
> Currently, it is difficult to combine these objects; `rbind()` can only
> combine
> objects with the same samples but different features/ranges and `cbind()`
> can only combine objects with the same features/ranges but different
> samples. I think it would be useful to have a "combine" method for `SE`
> objects that handles the situation where each object has different samples
> but with possibly non-overlapping features/ranges.
>
> I've written a first pass at a method to do this at
> https://gist.github.com/PeteHaitch/8993b096cfa7ccd08c13.
> Is this a method other people find themselves in need of and, if so, might we
> add something like this to the SummarizedExperiment package? As noted in
> the gist, there's a few things I'd like to address to make it more robust and
> complete (probably some optimisations too).
>
> Cheers,
> Pete
>
> [[alternative HTML version deleted]]
>
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