enrich_hmdb: enrich_kegg

In tidymass/metpath: Pathway analysis for metabolomics data

enrich_kegg

Description

Pathway enrichment for metabolomics.

Usage

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(s)

Xiaotao Shen [e-mail]

Examples

## Not run: 
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

## End(Not run)

tidymass/metpath documentation built on Sept. 24, 2022, 9:25 p.m.