ODCurveToFluxCurves {CoRegFlux} | R Documentation |
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.
ODCurveToFluxCurves(model, ODs, times, metabolites_rates = NULL, biomass_flux_index = get_biomass_flux_position(model))
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. |
An object FluxCurves to visualize using the function
visFluxCurves
visFluxCurves, ODCurveToMetabolicGeneCurves, visMetabolicGeneCurves
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)