PERTURBATION_analysis: PERTURBATION_analysis, a function for robustness analysis.

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

Description

Robustness analysis is described procedurally in the COBRA-ToolBox manual. This function encodes the basic principle of the procedure and returns the result as an X versus Y list and generates a plot on successful completion.

Usage

	PERTURBATION_analysis(reaction_number,fba_object,y_axis_rxn=NULL,
	plot_to_file=FALSE,write_FLD_file=FALSE,ret_FLD_matrix=FALSE)

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.
reaction_number	Reaction number of the reaction to be ramped down. This number may be obtained by using the function SEARCH_reaction for a text search through the FBA_obj-reaction list.
y_axis_rxn	Reaction to be plotted on the y axis in case it is not the objective fuction.
plot_to_file	Boolean indicating if the graph to be printed to a file.
write_FLD_file	The flux vector for each point of perturbation is stored into the columns of a matrix, this boolean indicates if that matrix should be written out to a tab-delimited file.
ret_FLD_matrix	The flux vector for each point of perturbation is stored into the columns of a matrix, this boolean indicates if that matrix should be added to the list returned by this function.

Examples

#Perturbation analysis of fluxes
data(Ecoli_core)
#Ec_xy_O2<-PERTURBATION_analysis(reaction_number=36,Ecoli_core)

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