[Bioc-devel] Help with class lost after subsetting.

Hervé Pagès hp@ge@ @ending from fredhutch@org
Tue Aug 28 20:46:50 CEST 2018

On 08/27/2018 11:01 PM, Martin Morgan wrote:
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_waldronlab_MultiAssayExperiment_blob_master_R_subsetBy-2Dmethods.R-23L261&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=BFHgkPpGkkRZx_me9V6pN2aTIxXYDgkUBG5jJTKLugc&s=6XrUMqkUrT5cepxjwAwSXVXdjOeyRdWAjdpGaasVqc0&e= 
> 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.

Yep. Personally I tend to prefer BiocGenerics:::replaceSlots()
over initialize() because the former can be called with check=FALSE
in order to skip a possibly expensive validation. So:

         ExperimentList = harmon[["experiments"]],
         colData = harmon[["colData"]],
         sampleMap = harmon[["sampleMap"]],
         metadata = metadata(x),
         check = FALSE)

If you know that the replacement values are valid (because of the way
you prepared them), then validation should not be needed.

Also when only **some** of the slots are updated (which is not the
case in the above example where all the slots are being replaced),
I find that the use of initialize() is misleading from a readability
point of view.

See https://stat.ethz.ch/pipermail/bioc-devel/2017-September/011496.html
for a discussion about this about 1 year ago.


> Martin
>> Best regards,
> _______________________________________________
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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