Hi @sarahi,
Thanks for the questions, for the errors - are you setting the genefamilies as row.names or are they a separate column (e.g. row.names(gfr) = grf$'Gene Families' - then remove the genefamilies column)? My best guess without playing with the data is that MaAsLin is tripping over the gene families column because it assumes that everything in the df should be numeric for the input data. If that doesn’t work - can you send a reproducible example, either here or to my email, so that I can replicate what you are seeing?
Yes - you can use all the HUMAnN output in MaAsLin - the interpretation of the pathway coverage is the only one that isn’t straightforward. Please see our tutorial for more examples of using MaAsLin on functional data. MaAsLin won’t tell you what is core to your samples but should be able to tell you what is differential.
Best,
Kelsey