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fmicompbio / einprot

Proteomics analysis workflows
https://fmicompbio.github.io/einprot/
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getUniProtToIDMapping or getConvTable? #25

Open skiaphrene opened 4 weeks ago

skiaphrene commented 4 weeks ago

Hi, this isn't really an issue, but a call for clarification... I don't think it's clear what the difference is between getUniProtToIDMapping() and getConvTable(). They clearly give different results, but I don't understand the difference from the manual pages.

I am working with C. elegans, so if I call: einprot::getUniProtToIDMapping("roundworm") I get a data.frame mapping UniProt IDs to Gene Names / Symbols.

If I call: einprot::getConvTable(type = "WormBase") I get a data.frame mapping UniProt IDs to WormBase IDs. The latter has more mappings.

I need to use both, of course! :-)

Would it make sense to have a function that returned both mappings? Or a single function that could return either mapping? Or if the underlying code is so different, explain that in the help files, and add each function as a "See also" entry in the help file? Would it make sense to unify the argument specifications to each (e.g. "C. elegans" for both)? Just some ideas for clarification!

csoneson commented 4 weeks ago

Yes, fair point - the functions were originally written for different purposes, but I think it can indeed be simplified. I'll add it to the list.