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

In ctlab/gatom: Finding an Active Metabolic Module in Atom Transition Network

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.