getMethods() not finding all methods

Hi Seth,

Thanks for the info - actually one of the things
I like about getMethods is seeing the function
internals - as you point out, geneNames is being
deprecated in favour of featureNames, which is
revealed by the guts of the geneNames method ;)

getMethods("geneNames")

An object of class ?MethodsList?
Slot "methods":
$ExpressionSet
Method Definition:

function (object)
{
    .Deprecated("featureNames")
    featureNames(object)
}
<environment: namespace:Biobase>

Signatures:
        object        
target  "ExpressionSet"
defined "ExpressionSet"




-----Original Message-----
From: r-devel-bounces at r-project.org on behalf of Seth Falcon
Sent: Thu 10/12/2006 5:28 PM
To: r-devel at stat.math.ethz.ch
Subject: Re: [Rd] getMethods() not finding all methods
 
"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

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