How to deal with assays without names?

fmicompbio / footprintR

Tools for working with single-molecule footprinting data

https://fmicompbio.github.io/footprintR/

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How to deal with assays without names? #12

Closed csoneson closed 1 month ago

csoneson commented 1 month ago

What should .getReadLevelAssayNames() return? The index of the assay(s)? What if some assays are named and others not?
Or should we just require that all assays are named (even though SummarizedExperiment doesn't impose such requirements)?

mbstadler commented 1 month ago

Good point! What about replacing .getReadLevelAssayNames() by .getReadLevelAssayIndices(), so we don't have to impose anything on top of SummarizedExperiment? It seems that the change would be not so big. .getReadLevelAssayNames() is only used three times: in .checkSEValidity, its unit test and subsetReads, and it seems to me that all these cases can also use an index returned from it.

csoneson commented 1 month ago

Yes, I think we can do that. We should probably add some tests for the functions that specify assay.type as well, to make sure they do the right thing.

csoneson commented 1 month ago

All assays are now required to be named, implemented in https://github.com/fmicompbio/footprintR/commit/4c51458376a686a78590422b1379031471f8010b