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 <[EMAIL PROTECTED]> 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@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
--
Martin T. Morgan
Bioconductor / Computational Biology
http://bioconductor.org
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