ODCurveToFluxCurves: ODCurveToFluxCurves

In CoRegFlux: CoRegFlux

Description

This function takes measured ODs and turn them into a FluxCurves object to be visualize using visFluxCurves(). It relies on flux variability analysis to highlight the flux value interval required to meet the specified OD.

Usage

ODCurveToFluxCurves(model, ODs, times, metabolites_rates = NULL,
  biomass_flux_index = get_biomass_flux_position(model))

Arguments

model	An object of class modelOrg, the metabolic model.
ODs	A vector of measured ODs
times	A vector of timepoints at which the flux balance analysis solution will be evaluated.
metabolites_rates	A data.frame containing the extraneous metabolites, their initial concentrations and their uptake rates. Columns must be named "names","concentrations" and "rates".
biomass_flux_index	Optional. index of the flux corresponding to the biomass reaction.

Value

An object FluxCurves to visualize using the function visFluxCurves

See Also

visFluxCurves, ODCurveToMetabolicGeneCurves, visMetabolicGeneCurves

Examples

data(iMM904)
ODs<-seq.int(0.099,1.8,length.out = 5)
times = seq(0.5,2,by=0.5)

metabolites_rates <- data.frame("name"=c("D-Glucose"),
"concentrations"=c(16.6),"rates"=c(-2.81))

ODtoflux<-ODCurveToFluxCurves(model = iMM904,
ODs = ODs,times = times, metabolites_rates = metabolites_rates)

visFluxCurves(ODtoflux)

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