[Bioc-devel] A method for combining SummarizedExperiment objects

Tue, Oct 20, 2015 1:30 AM

Hi Martin,

I've updated the gist in light of your very helpful feedback at
https://gist.github.com/PeteHaitch/8993b096cfa7ccd08c13 (the exact
revision at the time of writing is
https://gist.github.com/PeteHaitch/8993b096cfa7ccd08c13/375f39835b1855cf3b019f8fcaa65768475fc658).
There are still some design choices on which I would appreciate some
advice, as discussed in the link.

Thanks,
Pete

On 16 October 2015 at 07:26, Peter Hickey <peter.hickey at gmail.com> wrote:

Thanks for your feedback, Martin. I'll have a go at re-implementing
this and get back to the list next week.

Cheers,
Pete

On 16 October 2015 at 05:20, Morgan, Martin
<Martin.Morgan at roswellpark.org> wrote:

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

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