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
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:
BiocGenerics:::replaceSlots(x
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 = ..., ).
H.
I find that the use of initialize() is misleading from a readability
point of view.
See
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_2017-2DSeptember_011496.html&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=OlbCmHfOSsvIe5QU8cUQjnV7NeLHnJ9GndGatxMWmXQ&s=fV9PeZDYz9qEIxeLk00LcjpNNgzQy_kzi6aFEKBvlds&e=
for a discussion about this about 1 year ago.
H.
Martin
Best regards,
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: [email protected]
Phone: (206) 667-5791
Fax: (206) 667-1319
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