R devel - Oct 2006 - getMethods() not finding all methods

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.



> library(affy)
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

    Vignettes contain introductory material. To view, type
    'openVignette()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.

Loading required package: affyio
> 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"

$exprSet
Method Definition:

function (object) 
featureNames(object)
<environment: namespace:Biobase>

Signatures:
        object   
target  "exprSet"
defined "exprSet"


Slot "argument":
object

Slot "allMethods":
$ExpressionSet
Method Definition:

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

Signatures:
        object         
target  "ExpressionSet"
defined "ExpressionSet"

$exprSet
Method Definition:

function (object) 
featureNames(object)
<environment: namespace:Biobase>

Signatures:
        object   
target  "exprSet"
defined "exprSet"

> search()
 [1] ".GlobalEnv"        "package:affy"     
"package:affyio"    "package:Biobase"  
"package:tools"     "tools:RGUI"
 [7] "package:methods"   "package:stats"    
"package:graphics"  "package:grDevices"
"package:utils"     "package:datasets"
[13] "Autoloads"         "package:base"    
> getMethod("geneNames", "AffyBatch")
Method Definition:

function (object) 
{
    cdf.envir <- getCdfInfo(object)
    return(ls(env = cdf.envir))
}

Signatures:
        object     
target  "AffyBatch"
defined "AffyBatch"
> 



Steven McKinney

Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre

email: smckinney at bccrc.ca

tel: 604-675-8000 x7561

BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C. 
V5Z 1L3
Canada

"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