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CBIIT / R-cometsAnalytics

R package development for COMETS Analytics
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COMETS 1.3. Super-batch and Addition of metabolite meta-data table to zip file #25

Closed steven-moore closed 6 years ago

steven-moore commented 6 years ago

The results files are outputting correctly from COMETS-Analytics. However, to link the results from one cohort to another's, we need to pull in their metabolite meta-data table in its entirety, most likely as a separate table in the zip file. In addition, if the results auto-harmonized, we should also pull in the UID column, possibly one or two other columns.

Without meta-data or the UID, we cannot harmonize the metabolites on the back end. This is a high priority fix.

ellatemprosa commented 6 years ago

this can be part of the new super batch function. we need to just add the harmonization csv to the zip

wobenshain commented 6 years ago

To confirm, we're looking to add the csv from checkIntegrity to the zip file?

ellatemprosa commented 6 years ago

yes, and another file that will cover another requirement. i will commit the function to cover thiis issue https://github.com/CBIIT/R-cometsAnalytics/issues/26

steven-moore commented 6 years ago

Yes (just seconding Ella's comment above)

steven-moore commented 6 years ago

I have tested, and the whole input file is currently being passed through. This is the wrong functionality. The "SubjectMetabolites" and "SubjectData" tabs should first be extracted, then the remaining tabs should be passed onward. This is a critical priority.

steven-moore commented 6 years ago

OK, scratch the above comment, which is actually relevant to issue 29, not this one. This issue is now resolved since the harmonization file is being passed through appropriately.