fva_robustness: FVA_robustness, a function to determine the change in...

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

Description

FVA_robustness builds upon FLUX_VAR_ANALYSIS to give the user a convenient function to examine the change in network robustness caused by a user supplied mutation. Graphical results for absolute flux span comparisons may be expected in the working directory

Usage

FVA_robustness(fba_object, mutation)

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.

mutation

A reaction number obtained using the SEARCH_reaction,or in the non-lethal reaction "list" result of an Exhaustive_single_deletion run. This reaction will be deleted during the FVA analysis

Examples

#Mutant network robustness, removing Formate Exchange which has no effect 
#on fluxes 
data(Ecoli_core)	
#FVA_robustness(Ecoli_core,25)	

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