[Bioc-devel] dimnames of multidimensional assays in SummarizedExperiment

[Hervé Pagès]

Hi Pete,

I'll look into this. Thanks!

H.

On 02/10/2016 12:33 PM, Peter Hickey wrote:
> The assays slot in a SummarizedExperiment object supports elements
> with up to 4 dimensions [*]
>
> library(SummarizedExperiment)
> makeSE <- function(n) {
>    assay <- array(1:2^n,
>                   dim = rep(2, n),
>                   dimnames = split(letters[1:(2 * n)], seq_len(n)))
>    SummarizedExperiment(assay)
> }
> x <- makeSE(4)
>
> However, the "higher-order" dimnames of the assays aren't preserved
> when calling the `assays` or `assay` getters:
>
>> dimnames(assay(x, withDimnames = TRUE))
> [[1]]
> [1] "a" "e"
>
> [[2]]
> [1] "b" "f"
>
> [[3]]
> NULL
>
> [[4]]
> NULL
>
> This is despite the data still being available in the assays slot:
>
>> dimnames(x at assays[[1]])
> 1`
> [1] "a" "e"
>
> 2`
> [1] "b" "f"
>
> 3`
> [1] "c" "g"
>
> 4`
> [1] "d" "h"
>
> The following patch fixes this by only touching the rownames and
> colnames and not touching the "higher-order" dimnames. Seem
> reasonable?
>
> Index: R/SummarizedExperiment-class.R
> ===================================================================
>    --- R/SummarizedExperiment-class.R (revision 113505)
> +++ R/SummarizedExperiment-class.R (working copy)
> @@ -174,7 +174,10 @@
> {
>    assays <- as(x at assays, "SimpleList")
>    if (withDimnames)
>      -        endoapply(assays, "dimnames<-", dimnames(x))
>    + endoapply(assays, function(assay) {
>      +                    dimnames(assay)[1:2] <- dimnames(x)
>      +                    assay
>      +                })
>    else
>      assays
> })
>
> [*] In fact, the assay elements can have more than 4 dimensions when
> constructed, although subsetting with `[` isn't supported (possibly
> things other than subsetting break as well in this case).
>
> # No error
> y <- makeSE(5)
> y
>
> # Error
> y[1, ]
>
> Perhaps there should be a check in the constructor that all assay
> elements have < 5 dimensions?
>
> Cheers,
> Pete
>
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>

-- 
Hervé Pagès

Program in Computational Biology
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