Many many packages in the methylation business (methylation array or
MethylSeq) define dozens of data structures (S4 classes) for the purpose
of representing methylation data. Some of the most outstanding data
structures seem to be RnBeadSet in RnBeads, MethylSet in minfi,
MethyLumiSet in methylumi, BSdataSet in methylPipe, BSrel and BSraw in
BiSeq, etc... Some are SummarizedExperiment derivatives, some are eSet
derivatives, others don't extend anything and reimplement a lot of
things from scratch. I wonder if some kind of
unification/standardization effort has been considered. Would be great
to achieve some sort of consensus like has been done with
SingleCellExperiment for single cell data. Having the consensual classes
implemented in their own package, and separated from any particular
application like in the case of SCE, would help with exposure and
reusability.
For the context: I'm currently looking at a new submission (MAGAR) that
implements yet another set of S4 classes (methQTLInput and
methQTLResult) almost from scratch:
-
https://github.com/MPIIComputationalEpigenetics/MAGAR/blob/a5281222426441ed48581cd5b45d1d81d6537ed4/R/methQTLResult-class.R#L38-L57
-
https://github.com/MPIIComputationalEpigenetics/MAGAR/blob/a5281222426441ed48581cd5b45d1d81d6537ed4/R/methQTLResult-class.R#L38-L57.
I'm hoping that they can avoid that by reusing (either directly or by
extending) something that's already available in the ecosystem but it's
not clear to me what to recommend.
Thanks,
H.
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
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