[Bioc-devel] Help with class lost after subsetting.
mtmorg@n@bioc @ending from gm@il@com
Tue Aug 28 08:01:37 CEST 2018
On 08/28/2018 12:19 AM, Charles Plessy wrote:
> Dear Bioconductor developers,
> In the CAGEr package, I created a "CAGEexp" class that extends
> "MultiAssayExperiment" without adding new slots, in order to define generic
> functions that require CAGEr-specific contents in the colData slot.
> Unfortunately, when run in the development branch of Bioconductor,
> the CAGEexp objects lose their class when they are subsetted. Here
> is an example:
> A CAGEexp object of 4 listed
> A MultiAssayExperiment object of 4 listed
> This breaks examples in the package, as well as existing code.
> I am lost on how to troubleshoot this. May I ask for your help ?
I debugged this using first `selectMethod("[", "MultiAssayExperiment")`
and then `showMethod()` / `selectMethod()` to arrive at
The problem is that this line
returns a MultiAssayExperiment; what it should do is probably closer to
the 'copy constructor' functionality of `initialize()`, along the lines of
initialize(x, ExperimentList = ..., )
This could be opened as an issue on the MultiAssayExperiment github
repository; maybe Herve or Michael or others might comment on the best
> Best regards,
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