Steven McKinney wrote:
> Hi Seth,
>
> Thanks for the info - actually one of the things
> I like about getMethods is seeing the function
> internals 
Yes, that's why showMethods() has the option includeDefs=TRUE to include 
the definitions.  There are other options to look at multiple functions 
or specific classes.  Look at ?showMethods

And no, it's not a bug in getMethods(), which was never intended for 
human-readable output, but a side-effect of the changes for faster 
caching and dispatch in 2.4.0.  With the use of environments in place of 
the methods list objects (returned by getMethods()), getMethods() will 
probably be deprecated in the next version.

> - 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@r-project.org 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" <smckinney@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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