[Rd] getMethods() not finding all methods

[Seth Falcon]

"Steven McKinney" <smckinney at bccrc.ca> writes:

> Running R2.4.0 on Apple Mac OS X 10.4.8,
> in Emacs ESS mode, and also R.app.
>
>
> In an attempt to learn a bit more about
> a particular method (geneNames in package affy)
> I invoked
>
>   getMethods("geneNames")
>
> which produced geneNames methods, but not the
> one in affy (output below).
>
> I had to know the signature (AffyBatch) in order
> to find the method
>
>> getMethod("geneNames", "AffyBatch")
>
> Isn't getMethods() supposed to get them all?
>
> Is this a problem, or bug, or am I misunderstanding 
> something?
>
> I try to use getMethods() to learn how things work,
> without having to always get the source code and
> grep my way through the source.  Is there another
> way to get all methods that I should be using?
>
> Any info appreciated.

I think it may be a bug in getMethods.  At least, I would expect it to
show the AffyBatch method.  The output of showMethods is, IMO, more
readable and, in this case, more useful:

> library(affy)
[snip]
> showMethods("geneNames")
Function: geneNames (package Biobase)
object="AffyBatch"
object="ExpressionSet"
object="exprSet"

As an aside, geneNames is deprecated in favor of featureNames, a
somewhat more "P.C." term for the things measured on the chips :-)

Best,

+ seth