coregflux_static: Update the model using the provided gene regulatory network...
In CoRegFlux: CoRegFlux

Description Usage Arguments Value Examples

coregflux_static() uses the gene states to update the fluxes bounds from the metabolic model.

1 2	coregflux_static(model, predicted_gene_expression, gene_parameter = 0, tol = 1e-10, aliases = NULL)

`model`	A genome-scale metabolic model of class modelorg
`predicted_gene_expression`	The vector of predicted gene expression for the genes present in the metabolic model as given by `predict_linear_model_influence()`
`gene_parameter`	Parameter of the softplus function
`tol`	Fluxes values below this threshold will be ignored.
`aliases`	a data.frame containing the gene names currently used in the network under the colname "geneName" and the alias under the colnames "alias"

list containing:

`model`	the metabolic model with the coregflux constraints added
`softplus_positive`	the results of evaluating ln(1+exp(gpr(x+theta))) where gpr() are the continuous version of the gpr rules applied to a set of gene expression x
`softplus_negative`	the results of evaluating ln(1+exp(gpr(x+theta))) where gpr() are the continuous version of the gpr rules applied to a set of gene expression x

data("SC_GRN_1")
data("SC_experiment_influence")
data("SC_EXP_DATA")
data("aliases_SC")
data(iMM904)
data(PredictedGeneState)
static_list<-coregflux_static(iMM904,PredictedGeneState)