abcdeFBA (version 0.4)

BFD_Processor: BFD_Processor, a Bi-Flux-Del-Processor function

Description

BFD_Processor reassembles the "result(n)" files created by Exhaustive_double_deletion, the result files should be a complete set from 1-n and put in a folder BKO in pwd before execution. The output is a tab delimited spreadsheet Fatal_Double_knockouts_unique.xls

Usage

BFD_Processor(fba_object,EXSDR)

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.

EXSDR

A list of the type generated by the Exhaustive_single_deletion function, this list may be passed to this function or the function will generate the list on its own. It is used for removing the results of lethal single knockouts which will form pairs with all other knockouts leading to false positives of double synthetic lethality.

Examples

#Function to process the results of the double knockout
#data(Ecoli_core)	
#BFD_Processor(Ecoli_core,EXSDR=Exhaustive_single_deletion_results)	
# A prompt will appear asking for the number of simulation pieces 
#and also to make sure you have your results filled in a folder 
#called BKO in the present working directory.