FBA_solve: FBA_solve, a function to solve CBM problems

In abcdeFBA: ABCDE_FBA: A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package.

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 simulation, bounds specifies the lower and upper inequality constraints, rhs is the right hand side of the steady state expression, types refers to the numeric nature of the variables which in case of FBA happens to be "Continuous", max is a Boolean specifying the type of optimization, "Maximization" by default, all_genes is all the genes present in the model, gpr contains boolean expressions of gene essentiality for the corresponding reactions in the model, metabolite_name contains list of all the metabolites, reaction_list contains all the reactions present in the model, compartment is a numeric identifier for each reaction the key for which is in comp_name.
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)

abcdeFBA documentation built on May 2, 2019, 9:19 a.m.