enrich_pathways: Pathway Enrichment Analysis

In tidymass/metpath: Pathway analysis for metabolomics data

Pathway Enrichment Analysis

Description

This function performs pathway enrichment analysis using metabolic pathway databases. It supports compound and metabolite enrichment based on HMDB or KEGG identifiers.

Usage

enrich_pathways(
  query_id,
  query_type = c("compound", "protein"),
  id_type = c("HMDB", "KEGG"),
  pathway_database,
  only_primary_pathway = FALSE,
  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	A vector of compound or metabolite identifiers.
query_type	Character. Type of query, either '"compound"' or '"protein"'. Default: '"compound"'.
id_type	Character. Type of identifier, either '"HMDB"' or '"KEGG"'. Default: '"HMDB"'.
pathway_database	The pathway database object containing pathway information.
only_primary_pathway	Logical. Whether to filter only primary pathways. Default: 'FALSE'.
p_cutoff	Numeric. The significance threshold for pathway enrichment. Default: '0.05'.
p_adjust_method	Character. P-value adjustment method. Options include '"holm"', '"hochberg"', '"hommel"', '"bonferroni"', '"BH"', '"BY"', '"fdr"', '"none"'. Default: '"holm"'.
method	Character. Statistical method used for enrichment analysis. Options: '"hypergeometric"' or '"fisher"'. Default: '"hypergeometric"'.
threads	Integer. Number of threads to use for computation. Default: '3'.

Value

A data frame containing the pathway enrichment results, including pathway ID, pathway name, description, p-values, adjusted p-values, and mapping statistics.

Examples

## Not run: 
  data("sample_pathway_database") # Load example pathway database
  query_metabolites <- c("HMDB0000122", "HMDB0000532", "HMDB0000889")
  enrichment_results <- enrich_pathways(
    query_id = query_metabolites,
    query_type = "compound",
    id_type = "HMDB",
    pathway_database = sample_pathway_database,
    p_cutoff = 0.05,
    method = "fisher"
  )
  print(enrichment_results)

## End(Not run)

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