more functional importers (e.g. humann)

[antagomir]

Mappings are available for both UniRef90 and UniRef50 gene families to the following systems:

MetaCyc Reactions

KEGG Orthogroups (KOs) Pfam domains Level-4 enzyme commission (EC) categories EggNOG (including COGs) Gene Ontology (GO) Informative GO Source

File names usually like..

genefamilies_ec_uniref90_with_names_cpm.tsv genefamilies_ec_uniref90_with_names_relab.tsv

genefamilies_eggnog_regroup.tsv genefamilies_eggnog_uniref90_with_names_cpm.tsv genefamilies_eggnog_uniref90_with_names_relab.tsv

genefamilies_go_regroup.tsv genefamilies_go_uniref90_with_names_cpm.tsv genefamilies_go_uniref90_with_names_relab.tsv

genefamilies_ko_regroup.tsv genefamilies_ko_uniref90_with_names_cpm.tsv genefamilies_ko_uniref90_with_names_relab.tsv

genefamilies_level4ec_regroup.tsv

genefamilies_pfam_regroup.tsv

genefamilies_uniref90_with_names_cpm.tsv genefamilies_uniref90_with_names_relab.tsv genefamilies.tsv.gz genefamilies_unstratified.tsv

level4ec_names_norm.tsv.gz

map_eggnog_uniref90_with_names.tsv

map_go_uniref90_with_names.tsv

map_ko_uniref90_with_names.tsv

map_pfam_uniref90_with_names.tsv

map_uniref90_with_names.tsv

joined_pathcoverage.tsv

[antagomir]

mia already has importHUMAnN and ideally the other tables could be readily dealt with the same one, or at least share many parts of it. If the same function can be used, we could instead show how to import any of these using mia functions in the vignette.

[antagomir]

Some more issues with mia::importHUMAnN() are reported here