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