abcdeFBA (version 0.3)

PERTURBATION_analysis: PERTURBATION_analysis, a function for robustness analysis.

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 simulat

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)