enrich_hmdb: enrich_kegg

Description Usage Arguments Value Author(s)

View source: R/enrich_hmdb.R

Description

Pathway enrichment for metabolomics.

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
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 shenxt1990@outlook.com


tidymass/metpath documentation built on Jan. 14, 2022, 7:32 p.m.