[Bioc-devel] A method for combining SummarizedExperiment objects

Peter Hickey peter.hickey at gmail.com
Thu Oct 15 03:52:23 CEST 2015


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

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