update_fluxes_constraints_influence: Update the fluxes constraints to simulate TF KO or...

In CoRegFlux: CoRegFlux

Description

Update the constraints according to the influence & regulatory network for a single KO or over-expression

Usage

update_fluxes_constraints_influence(model, coregnet, regulator_table,
  aliases)

Arguments

model	An object of class modelOrg, the metabolic model.
coregnet	Object of class CoRegNet, containing the regulatory and coregulatory interactions.
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
aliases	Optional, a data.frame containing the gene names used in the metabolic model and the aliases to use to match the regulatory network

Value

Return the model with updated bounds

Examples

data("SC_GRN_1")
data("iMM904")
data("aliases_SC")
regulator_table <- data.frame("regulator" = "MET32",
                              "influence" = -1.20322 ,
                              "expression" = 3,
                              stringsAsFactors = FALSE)
model_TF_KO_OV_constraints <- update_fluxes_constraints_influence(
model= iMM904,coregnet = SC_GRN_1,regulator_table =  regulator_table,
aliases = aliases_SC)

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