ODCurveToFluxCurves: ODCurveToFluxCurves

Description Usage Arguments Value See Also Examples

View source: R/ODToGenes.R

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

1
2
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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
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.