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: [EMAIL PROTECTED] on behalf of Seth Falcon
Sent: Thu 10/12/2006 5:28 PM
To: r-devel@stat.math.ethz.ch
Subject: Re: [Rd] getMethods() not finding all methods
"Steven McKinney" <[EMAIL PROTECTED]> 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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