get_S_mats: Convert stoichiometric matrix to edge list of reactions

In borenstein-lab/mimosa2: Model-based Integration of Metabolite Observations and Species Abundances

Convert stoichiometric matrix to edge list of reactions

Description

Convert stoichiometric matrix to edge list of reactions

Usage

get_S_mats(
  all_mods,
  species_names,
  edge_list = F,
  get_bounds = T,
  remove_sinks = T
)

Arguments

all_mods	List of Cobra-formatted metabolic models
species_names	List of species names for each model
edge_list	Whether to return the metabolic network as a stoichiometric matrix or edge list
get_bounds	Whether to extract information on upper and lower bound constraints (only with edge list)
remove_sinks	Remove reactions that have NA as a substrate or product (usually uninformative transporters etc)

Value

Either a stoichiometric matrix or edge list of reactions

Examples

get_S_mats(all_mods, my_species, edge_list = T)

borenstein-lab/mimosa2 documentation built on Dec. 19, 2024, 12:44 a.m.