update_fluxes_constraints_geneKOOV: Update the fluxes constraints to simulate gene KO or...

In i3bionet/CoRegFlux: CoRegFlux

Description

Update the constraints of the reactions associated with the knock-out or overexpressed gene

Usage

update_fluxes_constraints_geneKOOV(model, gene_table, aliases = NULL)

Arguments

model	An object of class modelOrg, the metabolic model.
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
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("iMM904")
data("aliases_SC")
gene_table <- data.frame("gene" = c("YGL202W","YIL162W"),
"expression" =c(2,0), stringsAsFactors = FALSE)

model_gene_KO_OV_constraints <- update_fluxes_constraints_geneKOOV(
model= iMM904,
gene_table =  gene_table,
aliases = aliases_SC)

i3bionet/CoRegFlux documentation built on May 31, 2019, 1:50 a.m.