ODCurveToMetabolicGeneCurves: ODCurveToMetabolicGeneCurves

Description Usage Arguments Value Examples

View source: R/ODToGenes.R

Description

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.

Usage

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ODCurveToMetabolicGeneCurves(times, ODs, metabolites_rates = NULL, model,
  softplusParam = 0, singlePointFluxEstimate = FALSE,
  biomass_flux_index = get_biomass_flux_position(model),
  aliases = NULL)

Arguments

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.

Value

Metabolic genes curves to visualize using the function visMetabolicGeneCurves

Examples

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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")

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