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

[Hervé Pagès]

Hi Pete,

On 03/02/2016 12:42 PM, Peter Hickey wrote:
> 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.

Requiring that abind(..., along=1) and abind(..., along=2) work on
assays of dim > 2 would work. Note that abind() has a complicated
signature (many extra arguments) but the "abind" methods that one
would need to implement wouldn't need to satisfy the full abind()
contract (in the context of SummarizedExperiment assays, satisfying
the full contract is not needed and would be too much work).

Alternatively we can introduce our own generics for that e.g.
abind1() and abind2(), or arbind() and acbind() (for "assay rbind"
and "assay cbind"). Advantages: the signatures would be cleaner,
the contracts simpler, and the methods easier to implement. Also
we wouldn't need to depend on the abind package.

What do you think?

H.

>
> Cheers,
> Pete
>
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>

-- 
Hervé Pagès

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