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getMethods() not finding all methods

6 messages · Steven McKinney, John Chambers, Seth Falcon

Original
Steven McKinney
# 
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
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.
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
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"
[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"
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
Seth Falcon
# 
"Steven McKinney" <smckinney at bccrc.ca> writes:
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:
[snip]
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
Steven McKinney
# 
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 ;)
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:
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:
[snip]
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

______________________________________________
R-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Seth Falcon
# 
John Chambers <jmc at r-project.org> writes:
A feature request: it would be useful in the context of attempting to
build documentation helper tools to have a return value that was
more structured than what printTo=FALSE provides.
I was expecting a different result based on the first sentence in the
doc describing getMethods:

     The function 'getMethods' returns all the methods for a particular
     generic (in the form of a generic function with the methods
     information in its environment).

Hence, it surprises me that not all methods are returned.  Reading on
I now see:

     ... is not intended to be called directly.

So I guess I got what I deserve ;-)

+ seth