enrich_kegg

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 shenxt1990@outlook.com

Examples

if (FALSE) {
data("hmdb_pathway")
data("query_id_hmdb")

pathway_database =
  filter_pathway(object = hmdb_pathway, class = "Metabolic;primary_pathway")
hmdb_enrichment =
  enrich_hmdb(
    query_id = query_id_hmdb,
    query_type = "compound",
    id_type = "HMDB",
    pathway_database = pathway_database,
    only_primary_pathway = TRUE,
    p_cutoff = 0.05,
    p_adjust_method = "BH",
    method = "hypergeometric",
    threads = 5
  )

hmdb_enrichment
}