[Bioc-devel] cbind method / SummarizedExperiment

Martin Morgan mtmorgan at fhcrc.org
Wed Aug 20 21:30:27 CEST 2014

On 08/19/2014 08:50 AM, Hans-Ulrich Klein wrote:
> Hi all,
> I implemented a subclass of SummarizedExperiment from the GenomicRanges package.
> When I call cbind() on two objects of my subclass, I get an object of class
> SummarizedExperiment and not of my own class. So I have to re-implement cbind()
> in order to avoid this unwanted class coercing. This is not the case for, e.g.,
> combine() for class eSet. I am wondering whether it would make sense to change
> the implementation of cbind() (and also rbind() etc.) for SummarizedExperiment
> in order to make class inheritance more convenient?

Hi Hans -- Thanks for the report, this is fixed in 1.17.35 for cbind and rbind; 
if there are other methods with similar problems please don't hesitate to let us 

 > A = setClass("A", contains="SummarizedExperiment")
 > class(cbind(A(), A()))
[1] "A"
[1] ".GlobalEnv"
 > class(rbind(A(), A()))
[1] "A"
[1] ".GlobalEnv"


> Best,
> Hans
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