Skip to content

Possible bug in accessing methods documentation?

2 messages · Seth Falcon, Martin Morgan

Original
Seth Falcon
# 
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")
[1] "ExpressionSet"
attr(,"package")
[1] "Biobase"
[1] "AFFX-MurIL2_at"  "AFFX-MurIL10_at"
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
Martin Morgan
# 
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: