COMETS 1.3 Harmonization not consistently working

CBIIT / R-cometsAnalytics

R package development for COMETS Analytics

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COMETS 1.3 Harmonization not consistently working #21

Closed steven-moore closed 6 years ago

steven-moore commented 6 years ago

Sometimes the metabolites do not harmonize, even when HMDB IDs are present. To my understanding, Ella was looking into this issue. This also occurred with the R. Kelly VDAART file, which I can supply, if needed.

ellatemprosa commented 6 years ago

no problem. i will fix this

steven-moore commented 6 years ago

First pass harmonization is working reasonably well. This will need to be modified in future versions as we learn more from IMS about which harmonization strategies are working. For COMETS 1.3, though, the intended functionality is in place, so I will close.

ellatemprosa commented 6 years ago

I committed harmonization by hmdb id just now to branch ella_022118hmdbdescrip. we now have a masterhmdb to use as a look up for metabolites not harmonized by metid. if a variable name in metabolite meta data starts with hmdb, it assumes hmdb.