getMetabolicPathways: Generate list of metabolic pathways from Reactome and KEGG...

View source: R/annotation.R

getMetabolicPathwaysR Documentation

Generate list of metabolic pathways from Reactome and KEGG databases

Description

Generate list of metabolic pathways from Reactome and KEGG databases

Usage

getMetabolicPathways(
  universe,
  metGenes,
  keggOrgCode,
  threshold = 0.01,
  includeReactome = TRUE,
  includeKEGG = TRUE
)

Arguments

universe

list of genes

metGenes

list of metabolic genes

keggOrgCode

KEGG organism code, like mmu or hsa

threshold

threshold for Fisher test to filter out non-metabolic pathways

includeReactome

whether to include Reactome pathways (only works for Entrez ID universe)

includeKEGG

whether to include KEGG pathways and modules

Value

list of metabolic pathways for given organism and list of genes


ctlab/gatom documentation built on May 3, 2024, 3:44 p.m.