From smckinney at bccrc.ca  Fri Oct 13 03:39:06 2006
From: smckinney at bccrc.ca (Steven McKinney)
Date: Thu, 12 Oct 2006 18:39:06 -0700
Subject: [Rd] getMethods() not finding all methods
References: <0BE438149FF2254DB4199E2682C8DFEB01D555DF@crcmail1.BCCRC.CA>
	<m2wt75m54e.fsf@ziti.local>
Message-ID: <0BE438149FF2254DB4199E2682C8DFEB0235F920@crcmail1.BCCRC.CA>

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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[Rd] getMethods() not finding all methods
Steven McKinney