how to creat trans_alpha and trans_beta in genus level

[milyzhou]

Hi, LIU I created taxonomic table by HUMAnN3， I want to know that which level dose the trans_alpha and trans_beta use to analyze?and is it possible to restrct the analysis to the genus level?

Thank you

[ChiLiubio]

Hi @milyzhou, Theoretically, I think it is feasible to do trans_alpha and trans_beta at each taxonomic level or pathway level for HUMAnN results, depending on the explained question. To restrict the analysis to genus, you can use cal_abund function and rel = FALSE parameter to get the RPK table at genus level and recreate a microtable object using this table.

[milyzhou]

Thank you!
I tryed to builded it followed tutorial and it worked! dataset <- mpa2meco("buglist_clean.tsv", sample_table =metadata) test <- dataset$merge_taxa(taxa = "Genus") and I will follow you suggesstion check my table again.