ODCurveToMetabolicGeneCurves {CoRegFlux} | R Documentation |
This function takes measured ODs and turn them into a ODcurveToMetCurve object
to be visualize using visMetabolicGeneCurves()
. It relies on flux
variability analysis to highlight the flux value interval required to meet the
specified OD and to map it on the metabolic genes.
ODCurveToMetabolicGeneCurves(times, ODs, metabolites_rates = NULL, model, softplusParam = 0, singlePointFluxEstimate = FALSE, biomass_flux_index = get_biomass_flux_position(model), aliases = NULL)
times |
A vector of timepoints at which the flux balance analysis solution will be evaluated. |
ODs |
vector of measured ODs. |
metabolites_rates |
A data.frame containing the extraneous metabolites, their initial concentrations and their uptake rates. Columns must be named "names","concentrations" and "rates". |
model |
An object of class modelOrg, the metabolic model. |
softplusParam |
Softplus parameter identify through calibration. |
singlePointFluxEstimate |
Optional, logical. |
biomass_flux_index |
index of the flux corresponding to the biomass reaction. |
aliases |
Optional. A data.frame containing the gene names used in the metabolic model and the aliases to use to match the regulatory network. |
Metabolic genes curves to visualize using the function
visMetabolicGeneCurves
ODs<-c(0.4500000,0.5322392,0.6295079,0.7445529) data("aliases_SC","iMM904") ODcurveToMetCurve<-ODCurveToMetabolicGeneCurves(times = seq(0.5,2,by=0.5), ODs = ODs,model = iMM904,aliases = aliases_SC) visMetabolicGeneCurves(ODcurveToMetCurve,genes="YJR077C")