[Bioc-devel] Overloading subset operator for an S4 object with more than two dimensions

[Michael Lawrence]

I agree with Wolfgang that the semantics of [ are being violated here. It
would though help if you could be a little less vague about your intent.
What is this data structure going to store, how should it behave?

On Thu, May 14, 2015 at 3:35 AM, Christian Arnold <christian.arnold at embl.de>
wrote:

> Hi there,
>
> I am about to develop a Bioconductor package that implements a custom S4
> object, and I am currently thinking about a few issues, including the
> following:
>
> Say we have an S4 object that stores a lot of information in different
> slots. Assume that it does make sense to extract information out of this
> object in four different "dimensions" (conceptually similar to a
> four-dimensional object), so one would like to use the subset "[" operator
> for this, but extending beyond the "typical" one or two dimensions to 4:
>
> setClass("A",
> representation=representation(a="numeric",b="numeric",c="numeric",d="numeric"))
> a = new("A", a=1:5,b=1:5,c=1:5,d=1:5)
>
> Now it would be nice to do stuff like a[1,2,3:4,5], which should simply
> return the selected elements in slots a, b, c, and d, respectively. So
> a[1,2,3:4,5] would return:
>
> An object of class "A"
> Slot "a":
> [1] 1
>
> Slot "b":
> [1] 2
>
> Slot "c":
> [1] 3 4
>
> Slot "d":
> [1] 5
>
> This is how far I've come:
>
> setMethod("[", c("A", "ANY", "ANY","ANY"),
>           function(x, i, j, ..., drop=TRUE)
>           {
>             dots <- list(...)
>             if (length(dots) > 2) {
>               stop("Too many arguments, must be four dimensional")
>             }
>
>             # Parse the extra two dimensions that we need from the ...
> argument
>             k = ifelse(length(dots) > 0 , dots[[1]], c(1:5))
>             l = ifelse(length(dots) == 2, dots[[2]], c(1:5))
>
>             initialize(x, a=x at a[i],b=x at b[j],c=x at c[k],d=x at d[l])
>           })
>
> This works for stuff like a[1,2,3, 4], but fails with a general error if
> one of the indices is a vector such as a[1:2,2,3, 4] or a[1,2,3,4:5].
>
>
> So, in summary, my questions are:
> 1. Is there a reasonable way of achieving the 4-dimensional subsetting
> that works as a user would expect it to work?
> 2. Does it make more sense to write a custom function instead to achieve
> this, such as subsetObject() without overloading "[" explicitly? What are
> the Bioconductor recommendations here?
>
> I'd appreciate any help, suggestions, etc!
>
> Thanks,
> Christian
>
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