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ilia-kats / MuData

MuData-compatible storage for bioconductor's MultiAssayExperiment
https://ilia-kats.github.io/MuData/
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Name the X assay "X" #4

Open multimeric opened 1 year ago

multimeric commented 1 year ago

It doesn't seem to be required that all the assays are named, but I've noticed it breaks various downstream code if it is not. Most notably cbind(some_sce) will fail if not all assays are named.

ilia-kats commented 1 year ago

Makes sense, but an AnnData could, in principle, contain a layer named X. I would add a check if that's the case and some way to handle the collision, e.g. naming the main assay XX or main-X or something like that (also checking for collisions with the modified name)

multimeric commented 1 year ago

I take your point, I guess that could happen, although it would be a very weird and confusing AnnData file. I'm fairly sure that Zellkonverter just gives it the name "X", but any name is better than nothing.