Simulation_Step: Single simulation step
In CoRegFlux: CoRegFlux

Description Usage Arguments Value See Also

View source: R/DFBAsimulationFunctions.R

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.

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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)

`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.

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.

Simulation

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