subsetByAssay(), subsetByRow(), subsetByColumn() still around

[lwaldron]

Still defined in R/MultiAssayExperiment-methods.R, have man pages, and noted in MultiAssayExperiment show method, but are not exported. Vignette uses e.g. subset(MAE, "columns") instead, which I think is now the recommended way along with [.

[LiNk-NY]

The subsetBy* functions are used by the [ bracket method when subsetting a MultiAssayExperiment (see here). They are documented because they are generics. I may be able to change them to what they intend using signatures such as c("MultiAssayExperiment", "missing", "missing", "ANY") in the case of subsetByAssay for a bracket [ subset method.

[lwaldron]

What's confusing is that they are documented and also suggested in the MultiAssayExperiment show method, but are only available through triple colon :::. This seems not the norm to me, or have you seen other non-exported S4 generics documented?

[LiNk-NY]

We discussed removing ?subset,MultiAssayExperiment-method from the package and exporting subsetBy* functions