fva: FLUX_VAR_ANALYSIS, a function to perform a flux variability...

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

Description

FVA can indicate the decrease in network robustness caused by non-lethal deletions.

Usage

FLUX_VAR_ANALYSIS(fba_object,reactions,filename)

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.
reactions	subset of reaction numbers on which to perform FVA, if left empty, all reactions of the network will be subject to FVA
filename	A string which will be the name of the file containing the output of the FVA simulation

Examples

#Simple flux variability Analysis
data(Ecoli_core)
#FLUX_VAR_ANALYSIS(Ecoli_core, filename="Wt_FVA.xls")

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