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

Description Usage Arguments Value Examples

View source: R/CoregfluxFunctions.R

Description

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

Usage

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

Arguments

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"

Value

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

Examples

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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)

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