flux_coupling_raptor: determine flux coupling between reactions in a Gurobi model

In DikshantPradhan/FluxCouplingTools:

Description

determine flux coupling between reactions in a Gurobi model

Usage

flux_coupling_raptor(model, min_fva_cor = 0.9, fix_frac = 0.1,
  fix_tol_frac = 0.01, bnd_tol = 0.1, stored_obs = 4000,
  cor_iter = 5, cor_check = TRUE, reaction_indexes = c(),
  compare_mtx = FALSE, known_set_mtx = Matrix(data = FALSE, nrow = 1,
  ncol = 1, sparse = TRUE))

Arguments

model	Gurobi model
fix_frac	const value used in fixing flux at non-zero value
fix_tol_frac	maximum allowed error when determining whether flux for a reaction is fixed
bnd_tol	allowed error in comparing max & min flux
stored_obs	maximum number of flux instancecs to store
cor_iter	number of iterations after which correlation is considered in checking coupling
reaction_indexes	indexes for reactions to check; check all if empty
compare_mtx	boolean to indicate whether or not to couple known sets together if any individual reactions are coupled; FALSE by default
known_set_mtx	boolean matrix of known coupling between reactions
min_fva	minimum correlation value to test for coupling

Value

boolean matrix indicating whether reactions are coupled to each other (reactions are assigned to rows and columns)

DikshantPradhan/FluxCouplingTools documentation built on Aug. 27, 2019, 2:19 a.m.