metab_connect: BYPASS_REACTIONS_SUBSTRATE, to find the influx and efflux...

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

Description

this function computes the production and consumption fluxes available to a particular metabolite from the fba_object and returns a list of with elements Production and Consumption

Usage

BYPASS_REACTIONS_SUBSTRATE(substrate_number,fba_object,verbose)

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.
substrate_number	this is the metabolite number of interest which may be found by using the SEARCH_metabolite function
verbose	a boolean indicating if the name of the reactions should be printed to the terminal output, default is TRUE

Examples

#To find the Bypass Reactions for a Substrate
data(Ecoli_core)	
ATP_prod_consump<-BYPASS_REACTIONS_SUBSTRATE(17,Ecoli_core)

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