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
[Bioc-devel] A method for combining SummarizedExperiment objects
3 messages · Peter Hickey, Martin Morgan
Sorry, the URL may have been mangled. It's https://gist.github.com/PeteHaitch/8993b096cfa7ccd08c13 <https://gist.github.com/PeteHaitch/8993b096cfa7ccd08c13.>
On Thu, 15 Oct 2015 at 12:52 Peter Hickey <peter.hickey at gmail.com> wrote:
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
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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