enrich_kegg

Source: R/enrich_hmdb.R

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
)

Arguments

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

Value

The MSE analysis result.

Author

Xiaotao Shen shenxt@sioc.ac.cn