sing_del_flxme: SINGLE_DEL_FLUXOME, a function to generate comparative...

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

Description

To analyse the effect of reaction deletions on the fluxome requires a contextual visualization, simple plots give little insight on what the results of the simulation mean. This function uses the annotations inherent to SBML models and generates comparative overlapping fluxome bar graphs depicting the overlap/change in flux based on Sub-system wise classification and generates PDF's for the same. The color scheme is green for wild-type and red for mutant. Overlaps of red and green generate brown while overshot mutant fluxes show up as magenta-pink, also separate PDF's are generated for increased and decreased fluxes.

Usage

SINGLE_DEL_FLUXOME(fba_object, deletion_number)

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.

deletion_number

Reaction number of the reaction to be deleted. This number may be obtained by using the function SEARCH_reaction for a text search through the fba_object-reaction list.

Examples

#Compare the flux distributions of the mutant with the wild-type
data(Ecoli_core)	
#SINGLE_DEL_FLUXOME(Ecoli_core,36)	

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