enrich_hmdb: enrich_kegg
In jaspershen/metPath: Pathway analysis for metabolomics data

Description Usage Arguments Value Author(s)

Pathway enrichment for metabolomics.

enrich_hmdb(
  query_id,
  query_type = c("compound", "protein"),
  id_type = c("HMDB"),
  pathway_database,
  only_primary_pathway = TRUE,
  p_cutoff = 0.05,
  p_adjust_method = c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr",
    "none"),
  method = c("hypergeometric", "fisher"),
  threads = 3
)

`query_id`	The vector of query IDs.
`query_type`	"compound" or "gene"
`id_type`	HMDB
`pathway_database`	KEGG or other metabolomics pathway database.
`only_primary_pathway`	only_primary_pathway
`p_cutoff`	p_cutoff
`p_adjust_method`	p_adjust_method
`method`	Hypergeometric or fisher test.
`threads`	threads