abcdeFBA (version 0.4)

Exhaustive_single_deletion: Exhaustive_single_deletion, a function that deletes each reaction in the network one at a time and returns results describing reaction lethality

Description

This function takes the argument of type fba_object which would be a FBA object and performs an exhaustive deletion of all the reactions in the reaction network and returns a list of biomass generated for all the deletions, the sub-optimal deletions, the super-optimal deletions and non-lethal deletions, also generates a pdf containing a distribution of the fatal reactions according to their sub-systems and a histogram of the biomass distribution for each deletion.

Usage

Exhaustive_single_deletion(fba_object,reactions,plot_to_file)

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

is a vector containing the reaction numbers to be deleted,if none are supplied all the reactions in the model are deleted iteratively.

plot_to_file

is a boolean indicating if a PDF output of the results of the single deletion should be made.

Examples

#Performing an exhaustive single reaction deletion
data(Ecoli_core)
#Results<-Exhaustive_single_deletion(Ecoli_core)