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:
CAGEr::exampleCAGEexp
A CAGEexp object of 4 listed
(...)
CAGEr::exampleCAGEexp[,1]
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
`subsetByColData,MultiAssayExperiment,ANY-method`.
The problem is that this line
https://github.com/waldronlab/MultiAssayExperiment/blob/master/R/subsetBy-methods.R#L261
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
implementation.
Martin
Best regards,
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