Simulation_Step: Single simulation step

Description Usage Arguments Value See Also

View source: R/DFBAsimulationFunctions.R

Description

Single simulation step in which fluxes are reconstrained according to metabolite concentrations, then given the continuous evaluation of the gpr rules and the softplus function of the gene regulatory state.

Usage

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Simulation_Step(model, coregnet, metabolites, met_concentrations_t0,
  biomass_t0, regulator_table, gene_table, time_step, gene_state,
  softplus_parameter, aliases, biomass_flux_index)

Arguments

model

An object of class modelOrg, the metabolic model.

coregnet

Optional, object of class CoRegNet object containing the information about regulatory and coregulatory relationships

metabolites

data frame of metabolites names

met_concentrations_t0

data frame of metabolites concentrations at t0, before performing a time step

biomass_t0

biomass at t0 before performing a step

regulator_table

A data.frame containing 3 columns: "regulator", "influence","expression" containing respectively the name of a TF present in the CoRegNet object as string, its influence in the condition of interest as a numerical and an expression factor of 0 for a KO, or an integer >1 for an overexpression

gene_table

A data.frame containing 2 columns: "gene", "expression" containing respectively the name of a gene present in the CoRegNet object as string and an expression factor of 0 for a KO, or an integer >1 for an overexpression

time_step

size of the time step to perform; that is t1-t0

gene_state

data frame with rows being gene names and columns being the gene expression or any other continuous value representing metabolites activity to be evaluated using the gpr rules

softplus_parameter

Softplus parameter identify through calibration. Default to 0.

aliases

Optional. A data.frame containing the gene names currently used in the network under the colname "geneName" and the alias under the colnames "alias"

biomass_flux_index

index of the flux corresponding to the biomass reaction.

Value

list of: fluxes: fluxes of the resulting fba soulution to the metabolic and genetic constraints biomass_yield: biomass yield that is used as proxy for the growth rate in the dynamic flux balance analysis solution. Corresponds to the flux of the biomass reaction of the model.

See Also

Simulation


CoRegFlux documentation built on Nov. 8, 2020, 5:21 p.m.