With HUMAnN3, I got the result of the KEGG KO annotation (by humann_regroup_table).
What do I need to do if I want to get the KEGG module annotation result? Maybe using R?
I did not find the relevant guidance/instruction, only the methods on KEGG pathway enrichment analysis (by other tools) !
Thanks a lot!
Any help will get me out of trouble!
HUMAnN 2 and 3 do not bundle KEGG pathway/module definitions, so we can’t directly quantify those functions from within HUMAnN. If you can download the module definitions and adapt them to HUMAnN’s format you could then run HUMAnN with your KOs as input and point to those pathway definitions to quantify them.
Thank you very much! However, how can I run HUMAnN with KOs as input and obtain KEGG pathway/module? I didn’t find code to conduct the procedure.
Yes, you would need to supply a file of KEGG pathway/module definitions to HUMAnN to do this though. That is not a file we currently bundle with the software.