model_to_pathway_sif: 'model_to_pathway_sif'

In saezlab/ocean: metabolic enzyme enrichment analysis

model_to_pathway_sif

Description

This function generate a subreaction network in sif format from the recon_redhuman model for a given set of pathways

Usage

model_to_pathway_sif(
  pathway_to_keep,
  pathways = recon2_redhuman$pathway,
  rxns = recon2_redhuman$rxns,
  rules = recon2_redhuman$rules,
  minmax = recon2_redhuman$minmax,
  stochio = recon2_redhuman$stochio,
  metab = recon2_redhuman$metab,
  mapping = recon2_redhuman$gene_mapping,
  recon1_metabolites = recon2_redhuman$metab_mapping
)

Arguments

pathway_to_keep	character vector with the ID of the pathways that should be used to build the SIF reaction network. Use "View(unique(recon2_redhuman$pathway))" to see available pathway IDs
pathways	pathway corresponding to redhuman reaction indexes
rxns	reaction IDs corresponding to redhuman reaction indexes
rules	gene rules corresponding to redhuman reaction indexes
minmax	min max flux boundaries corresponding to redhuman reaction indexes
stochio	redhuman stochiometric matrix
metab	metabolite IDs corresponding to redhuman metabolite indexes
mapping	obsolete
recon1_metabolites	obsolete

Value

a subreaction network in sif format

saezlab/ocean documentation built on Nov. 12, 2024, 5 a.m.