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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