[Bioc-devel] showMethods

Martin Morgan mtmorgan at fhcrc.org
Tue Sep 18 18:08:38 CEST 2012

On 09/18/2012 07:18 AM, Kasper Daniel Hansen wrote:
> Kind of a embarrasing question.  How do I see all methods defined for
> a given class?  I always thought I should use
>    showMethods(class = "SummarizedExperiment")
> but the output is clearly broken somehow with many things like

It helps to specify where the methods you're interested in come from 
(although this partly defeats the purpose)

   showMethods(class="SummarizedExperiment", where="package:GenomicRanges")

This would seem to be a bug in R and could be reported to R-devel

> Function "yieldSize":
>   <not an S4 generic function>
> I have known about this for a long time, but I never figured out the
> cause.  What is people doing for this?
> Update:  It seems that this may be caused by methods in imported
> packages, for example yieldSize is a method defined in Rsamtools.
> When I explicitely do library(Rsamtools) I don't get yieldSize in the
> output of showMethods(class = "SummarizedExperiment")
> Kasper
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