abcdeFBA (version 0.4)

DEGREE_MEASURE: DEGREE_MEASURE, measures the in-degree and out-degree of the metabolites in the network.

Description

this is a simple function to determine the degree measure, it uses the fba_object and computes and writes the measures to disk as a tab-separated spreadsheet

Usage

DEGREE_MEASURE(fba_object,file="Degree_measure")

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.

file

a filename for the tab delimited output file which is generated by this function

Examples

#Determining the Degree Measure of the Core E.coli Metabolic Network
data(Ecoli_core)	
#DEGREE_MEASURE(fba_object=Ecoli_core)