[Bioc-devel] Behaviour of rbind/cbind on assays slot of SummarizedExperiment with multidimensional assays

[Peter Hickey]

This is mostly directed to Herve and/or Martin, but I'd be interested
in other's input too.

The SummarizedExperiment package defines rbind,Assays-method and
cbind,Assays-method that are called when rbind() or cbind() is called
on a SummarizedExperiment object. In the case of two-dimensional assay
(matrix) these work much as if rbind/cbind were called on the matrix:

> library(SummarizedExperiment)
> m <- matrix(rnorm(100), nrow = 4, ncol = 25)
> se1 <- SummarizedExperiment(m)
> dim(assay(rbind(se1, se1)))
[1]  8 25
> dim(rbind(assay(se1), assay(se1)))
[1]  8 25
> dim(assay(cbind(se1, se1)))
[1]  4 50
> dim(cbind(assay(se1), assay(se1)))
[1]  4 50

When an assay is an array with more than 2 dimensions, however, the
result of the rbind,Assay-method (resp. cbind,Assays-method) differs
from the rbind,array-method (resp. cbind,array-method). This is for a
good reason because it preserves the dimensionality of the assay in
the SummarizedExperiment object. So in fact the "rbind(...)" of the
assay is more like abind::abind(..., along = 1) and the "cbind(...)"
of the assay is more like abind::abind(..., along = 2):

> x <- array(rnorm(100), dim = c(4, 5, 5))
> se2 <- SummarizedExperiment(x)
> dim(assay(rbind(se2, se2)))
[1] 8 5 5
> dim(rbind(assay(se2), assay(se2)))
[1]   2 100
> dim(abind::abind(assay(se2), assay(se2), along = 1))
[1] 8 5 5
> identical(assay(rbind(se2, se2)), abind::abind(assay(se2), assay(se2), along = 1))
[1] TRUE
> dim(assay(cbind(se2, se2)))
[1]  4 10  5
> dim(cbind(assay(se2), assay(se2)))
[1] 100   2
> dim(abind::abind(assay(se2), assay(se2), along = 2))
[1]  4 10  5
> identical(assay(cbind(se2, se2)), abind::abind(assay(se2), assay(se2), along = 2))
[1] TRUE

rbind/cbind does not work for other "array-like" objects with > 2
dimensions in the assays slot of a SummarizedExperiment because the
internal function SummarizedExperiment:::.bind_assay_elements()
constructs a new array via array() if the assay has more than 2
dimensions, thus destroying the original class of the array-like
object.

What I'm wondering is whether there is a way to generalise rbind/cbind
of Assays to other array-like objects provided that have a suitable
method defined. It seems to me that a good candidate would be to
require that an object in the assays slot has an abind(..., along = 1)
and abind(..., along = 2) method defined if it has more than 2
dimensions. It might even be worth using abind::abind() for when the
assay is an array with more than 2 dimensions to simplify the code
somewhat.

Thoughts? I'd be happy to work on a patch.

Cheers,
Pete