update_fluxes_constraints_influence {CoRegFlux} | R Documentation |
Update the constraints according to the influence & regulatory network for a single KO or over-expression
update_fluxes_constraints_influence(model, coregnet, regulator_table, aliases)
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 |
Return the model with updated bounds
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)