[Bioc-devel] Virtual class for `matrix` and `DelayedArray`? (or better strategy for dealing with them both)

Tim Triche, Jr. tim.triche at gmail.com
Mon Apr 30 16:42:35 CEST 2018

Don't do that.  Seriously, just don't.



On Mon, Apr 30, 2018 at 10:02 AM, Elizabeth Purdom <
epurdom at stat.berkeley.edu> wrote:

> Hello,
> I am trying to extend my package to handle `HDF5Matrix` class ( or more
> generally `DelayedArray`). I currently have S4 functions for `matrix`
> class. Usually I have a method for `SummarizedExperiment`, which will call
> call the method on `assay(x)` and I want the method to be able to deal with
> if `assay(x)` is a `DelayedArray`.
> Most of my functions, however, do not require separate code depending on
> whether `x` is a `matrix` or `DelayedArray`. They are making use of
> existing functions that will make that choice for me, e.g. rowMeans or
> subsetting. My goal right now is compatibility, not cleverness, and I'm not
> creating HDF5 methods to handle other cases. (If something doesn't
> currently exist, then I just enclose `x` with `data.matrix` or `as.matrix`
> and call the matrix into memory — for cleanliness and ease in updating with
> appropriate methods in future, I could make separate S4 functions for these
> specific tasks to dispatch, but that's outside of the scope of my
> question). So for simplicity assume I don't really need to dispatch *my
> code* -- that the methods I'm going to use do that.
> The natural solution for me seem to use `setClassUnion` and I was
> wondering if such a virtual class already exists? Or is there a better way
> to handle this?
> Here's a simple example, using `rowMeans` as my example:
> ```
> setGeneric("myNewRowMeans", function(x,...) { standardGeneric("
> myNewRowMeans")})
> setClassUnion("matrixOrDelayed",members=c("matrix", "DelayedArray"))
> #' @importFrom DelayedArray rowMeans
> setMethod("myNewRowMeans",
>           signature = "matrixOrDelayed",
>           definition = function(x,...){
>                         # a lot of code independent of x
>                         print("This is a lot of code shared regardless of
> class of x\n")
>                         # a lot of code that depends on x, but is
> dispatched by the functions called
>                         out<-rowMeans(x)
>                         #a lot of code based on output of out
>                         out<-out+1
>                         return(out)
>                 }
> )
> ```
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