Make longFormat a generic

[lgatto]

Would you consider making longFormat() a generic function (ideally in BiocGenerics) to allow implementation if different methods?

Currently, you have

MultiAssayExperiment::longFormat
function (object, colDataCols = NULL, i = 1L) 
{
    if (is(object, "ExperimentList")) 
        return(do.call(rbind, .longFormatElist(object, i = i)))
    else if (!is(object, "MultiAssayExperiment")) 
        return(.longFormatANY(object, i = i))
    if (any(.emptyAssays(experiments(object)))) 
        object <- .dropEmpty(object, warn = FALSE)
    longDataFrame <- do.call(function(...) rbind(..., make.row.names = FALSE), 
        .longFormatElist(experiments(object), i = i))
    longDataFrame <- .mapOrderPrimary(longDataFrame, sampleMap(object))
    if (!is.null(colDataCols)) 
        longDataFrame <- .matchAddColData(longDataFrame, colData(object), 
            colDataCols)
    as(longDataFrame, "DataFrame")
}
<bytecode: 0x5c13c5da9e48>
<environment: namespace:MultiAssayExperiment>

The QFeatures class extends MultiAssayExperiment, and has

QFeatures::longFormat
function (object, colvars = NULL, rowvars = NULL, index = 1L) 
{
    if (!is.null(rowvars)) {
        rdNames <- rowDataNames(object)
        misNames <- sapply(rdNames, function(x) any(!rowvars %in% 
            x))
        if (any(misNames)) 
            stop("Some 'rowvars' not found in assay(s): ", paste0(names(misNames)[misNames], 
                collapse = ", "))
        longDataFrame <- MultiAssayExperiment::longFormat(object, 
            colvars, index)
        rds <- lapply(rowData(object), function(rd) rd[, rowvars, 
            drop = FALSE])
        rds <- do.call(rbind, rds)
        cbind(longDataFrame, rds[as.character(longDataFrame$rowname), 
            , drop = FALSE])
    }
    else {
        MultiAssayExperiment::longFormat(object, colvars, index)
    }
}
<bytecode: 0x5c13df3029a0>
<environment: namespace:QFeatures>

The main advantage is support for variables from colData and rowData to the long format output (which is very handy).

The main motivation for this request is that I would also like to be able to convert SummarizedExperiment objects to long format.

[lgatto]

• Now that I look into it more carefully, MultiAssayExperiment::longFormat() isn't a method, but works on SEs calling MultiAssayExperiment:::.longFormatANY(). What is the reason for not using methods to handle this?
• And my second/other request would be to support rowData variables.