From mtmorgan at fhcrc.org  Thu Oct 12 00:04:05 2006
From: mtmorgan at fhcrc.org (Martin Morgan)
Date: Wed, 11 Oct 2006 15:04:05 -0700
Subject: [Rd] Possible bug in accessing methods documentation?
In-Reply-To: <m2ac423cz9.fsf@ziti.local> (Seth Falcon's message of "Wed, 11
	Oct 2006 11:48:42 -0700")
References: <m2ac423cz9.fsf@ziti.local>
Message-ID: <6phd58ymrvu.fsf@gopher4.fhcrc.org>

Seth's example is really good -- ExpressionSet extends eSet, and
featureNames is defined on eSet rather than ExpressionSet. To live
up to the documentation, we should end up at the help page with
\alias{featureNames,eSet-method}. A simpler example from the same
package is

?exprs(sample.ExpressionSet)

which should take us to the page with
\alias{exprs,ExpressionSet-method}. 

Probably related to the overall issue,

method ? exprs("ExpressionSet")
method ? featureNames("ExpressionSet") # inheritance

do not work.  Also, in the examples for ?"?"

methods ? combo

should probably be

method ? combo

Martin

Seth Falcon <sfalcon at fhcrc.org> writes:

> Hi,
>
> Reading help("Documentation"), I'm led to believe that a help call
> like:
>
>     ?myFun(x, sqrt(wt))
>
> Will search for help on the appropriate method in the case that myFun
> is generic.  This isn't working for me.  Here is an example using the
> Biobase package:
>
> ## If Biobase is not installed
> source("http://bioconductor.org/biocLite.R")
> biocLite("Biobase")
>
>> library("Biobase")
>> data(sample.ExpressionSet)
>> class(sample.ExpressionSet)
> [1] "ExpressionSet"
> attr(,"package")
> [1] "Biobase"
>> z <- featureNames(sample.ExpressionSet)
>> z[1:2]
> [1] "AFFX-MurIL2_at"  "AFFX-MurIL10_at"
>> ?featureNames(sample.ExpressionSet)
> Warning message:
> no method defined for function 'featureNames' and signature 'object = "missing"' in: .helpForCall(e1Expr, parent.frame()) 
> Error in .helpForCall(e1Expr, parent.frame()) : 
>         no documentation for function 'featureNames' and signature 'object = "missing"'
>
>
> Am I expecting the wrong thing or is this broken?  
>
> + seth
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

-- 
Martin T. Morgan
Bioconductor / Computational Biology
http://bioconductor.org




[Rd] Possible bug in accessing methods documentation?
Martin Morgan