change_obj_function: CHANGE_OBJ_FUNCTION, a function to change the objective for...

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

Description

a function akin to the COBRA function to change the objective function for FBA

Usage

CHANGE_OBJ_FUNCTION(obj_reaction,fba_object,new_wt,old_wt)

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.
obj_reaction	a reaction number which is to be made the new objective function; retrieved using the SEARCH reaction function
new_wt	the weight of the new objective, defaults to 1 but can be any number from 0~1
old_wt	the weight of the old objective, defaults to 0 but can be any number from 0~(1-new_obj_weight) or any other co-efficient if you wish for a customized objective function.

Examples

#To change the objective function of the model.
data(Ecoli_core)
ec_new_obj<-CHANGE_OBJ_FUNCTION(11,Ecoli_core,0.5,0.5)
#ec_new_obj will be identical to the Ecoli_core model except that 
#the objective function would change
FBA_solve(ec_new_obj)

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