enrich_kegg: enrich_kegg

In tidymass/metpath: Pathway analysis for metabolomics data

enrich_kegg

Description

Pathway enrichment for SMPDB database.

Usage

enrich_kegg(
  query_id,
  query_type = c("compound", "gene"),
  id_type = c("KEGG"),
  pathway_database,
  p_cutoff = 0.05,
  p_adjust_method = c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr",
    "none"),
  method = c("hypergeometric", "fisher"),
  threads = 3
)

Arguments

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

Value

The MSE analysis result.

Author(s)

Xiaotao Shen [e-mail]

tidymass/metpath documentation built on June 1, 2025, 10:05 p.m.