fvarLabels-like accessor for MAE

[lgatto]

I hope I haven't missed this functionality, but wouldn't it be useful to have an accessor that returns a list of rowData colnames, similar to colnames(mae) and rownames(mae). I personally find it useful to easily find out what these assay's rowData contain.

In Biobase, this function is called fvarLabels. Other possible names would be rowVarLabels or rowDataNames to stick with the new naming conventions.

It this is deemed of interest, I am happy to contribute such a generic and the method for the MultiAssayExperiment class. Something along the lines of

> rowDataNames
function(x) {
    CharacterList(lapply(experiments(x),
                         function(xx) 
                             tryCatch(colnames(rowData(xx)),
                                      error = function(e) NA_character_)))
}
> rowDataNames(mae)
CharacterList of length 4
[["Affy"]] character(0)
[["Methyl450k"]] <NA>
[["RNASeqGene"]] <NA>
[["GISTIC"]] character(0)

but that also handles the eSet cases.

[lwaldron]

I wonder if we should export a derivative class for MultiAssayExperiment that guarantees that all ExperimentList elements inherit from SummarizedExperiment. That would simplify adding functionality like subsetting on element rowData or colData, without writing messy exceptions for eSet and any other non-SummarizedExperiment element. It would then be the user's responsibility to replace any eSet elements using as(eset, "SummarizedExperiment").

[lwaldron]

@LiNk-NY, thoughts? Another option is to write some functionality for SummarizedExperiment elements that either drops or ignores non-SummarizedExperiment elements, depending on a drop argument.

[lgatto]

I wouldn't mind having an SE-only class (at the moment, at least), but this shouldn't become too restrictive in the future. If there are only SE, eSet and matrix objects to deal with, this could be enough in a first instance, with improvements only if required by relevant use-cases.

rowDataNames <- function(object) {
    stopifnot(inherits(object, "MultiAssayExperiment"))
    CharacterList(lapply(experiments(object),
                         function(x) {
                             if (inherits(x, "SummarizedExperiment"))
                                 colnames(rowData(x))
                             else if (inherits(x, "eSet"))
                                 colnames(Biobase::fData(x))
                             else NA_character_
                         }))
}

[LiNk-NY]

Hi Levi and Laurent, @lwaldron @lgatto

I think it would be good to have a derivative class that ensures that all elements in the ExperimentList are SummarizedExperiment. It would clean up and simplify operations that will then work seamlessly across the SummarizedExperiments.
Coercion could have the option of dropping any non-SummarizedExperiment elements with a warning.

Best,
Marcel

[LiNk-NY]

Any thoughts Martin? @mtmorgan

[mtmorgan]

I don't know what the problem being addressed is. The 'lesson' from SummarizedExperiment seemed to be that it was better to define the 'api' required (anything with a dim() / dimnames() / [,]) rather than class ('must be a matrix') provided more flexibility.