[Bioc-devel] BiocGenerics proposal

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Mon Mar 5 17:28:38 CET 2012

I agree with Steve; we should have ... on all generics just in case.

One disadvantage is that there is better argument checking without the
..., but I think we can live with that.  Steve's use case "I am now in
a different situation from the original author and I need more
flexibility" is, in my experience, not uncommon.


On Mon, Mar 5, 2012 at 11:05 AM, Steve Lianoglou
<mailinglist.honeypot at gmail.com> wrote:
> Hi,
> I think this has come up before (maybe even by me in some tangential
> way (probably related to the strand generic)) but I think it would be
> a "friendly" thing to do to define generics w/ the `...` argument
> after all the args we *think* people might want to use, because we
> can't really anticipate every way which people will eventually use
> things.
> For instance, the `strand` generic is just `strand(x)`, and you might
> say to yourself: "Self, when would you ever want to use the ... in a
> call to strand?" and a voice from afar might say "You would never."
> But we know that we should never say never, and really ... is it any
> skin off of our backs/noses to include this extra concession?
> I'm currently being bit by the `counts` generic in DE(X)Seq, which
> I've defined in my own package but it takes extra args, now I've got
> to go hacking my stuff, or hack the DEXSeq source to add a `...` to
> its counts generic that I guess I need to import now.
> Now you say "why would you need extra args?"
> Then I'd say, just for example, "Imagine you had something like a
> SummarizedExperiment-like object and you want the counts per 'event'
> or summarized by 'gene'", so I have an option to pull a `counts(x,
> by="gene")` maneuver.
> So:
> * How does the court feel about this general sentiment? Are there any
> reasons to strongly *avoid* doing this?
> * Can we add `...` to the strand generic, eg:
>  setGeneric("strand", function(x, ...) standardGeneric("strand"))
> * Can we add `counts(x, ...)` to BiocGenerics, while we're at it?
> Thanks,
> -steve
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
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