[Bioc-devel] A method for combining SummarizedExperiment objects

[Morgan, Martin]

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 at 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:bioc-devel-bounces at r-project.org] On Behalf Of
> Peter Hickey
> Sent: Wednesday, October 14, 2015 9:52 PM
> To: bioc-devel at r-project.org
> 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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