[Bioc-devel] Help with class lost after subsetting.
hp@ge@ @ending from fredhutch@org
Tue Aug 28 21:07:50 CEST 2018
On 08/28/2018 11:46 AM, Hervé Pagès wrote:
> 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
>>> 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 `subsetByColData,MultiAssayExperiment,ANY-method`.
>> 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
> 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),
ERRATA: It seems that MultiAssayExperiment have one more slot,
the "drops" slot, that the code above does not modify so this would
be one more reason IMO to use BiocGenerics:::replaceSlots() instead
of something like initialize(x, ExperimentList = ..., ) or
new(class(x),ExperimentList = ..., ).
> I find that the use of initialize() is misleading from a readability
> point of view.
> for a discussion about this about 1 year ago.
>>> Best regards,
>> Bioc-devel using r-project.org mailing list
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