abcdeFBA (version 0.2)

FBA_solve: FBA_solve, a function to solve CBM problems

Description

This function sugar-coats Rglpk_solve_LP which is a function provided by the Rglpk package, FBA_solve solves FBA problems using Rglpk_solve_LP and gives the solver output in a CBM context including solver error messages and graceful degradation.

Usage

FBA_solve(fba_object, precision,verbosity,maximize)

Arguments

fba_object

Is a list containing the data required to perform flux balance analysis. The elements of the list are mat which is the stoichiometric matrix, dir which gives the direction of the equality constraints, obj specifies the objective function for the simu

precision

A number indicating the precision of the flux solution after the decimal point, defaults to 6

verbosity

is a Boolean indicating if the verbose output of the LP solver should be displayed during simulation, defaults to FALSE

maximize

is a Boolean that can over-ride the default mode of optimization (maximization) and minimize if FALSE

Examples

# Flux Balance Analysis performed on a core-metabolism model of E.coli
	data(Ecoli_core)
	FBA_solve(fba_object=Ecoli_core,precision=6,verbosity=FALSE,maximize=TRUE)