sybil (version 2.0.0)

oneFluxDel: Single Flux Deletion Experiment

Description

Single reaction (flux) deletion analysis.

Usage

oneFluxDel(model, react = c(1:react_num(model)),
             lb = rep(0, length(react)),
             ub = rep(0, length(react)),
             checkOptSolObj = FALSE, ...)

Arguments

model

An object of class '>modelorg.

react

An object of class '>reactId or character or integer containing reaction id's to constrain to zero one by one. Default: all reactions present in argument model.

lb

A numeric vector of the same length as react containing the lower bounds for the reaction rates of reactions (variables) given in argument react. Default: 0 for all reactions in react, zero flux through all reactions.

ub

A numeric vector of the same length as react containing the lower bounds for the reaction rates of reactions (variables) given in argument react. Default: 0 for all reactions in react, zero flux through all reactions.

checkOptSolObj

A single logical value. If set to TRUE, a warning will be generated, if not all optimizations ended successful. Default: FALSE.

…

Further arguments passed to optimizer. Important ones are algorithm in order to set the algorithm to use or solverParm in order to set parameter values for the optimization software.

Value

An object of class '>optsol_fluxdel.

Details

The function oneFluxDel studies the effect of constraining single fluxes to zero flux rates on the phenotype of the metabolic network. The function performs \(n\) optimizations with \(n\) being the number of reaction id's given in argument react. Each optimization corresponds to the removal of one reaction.

See Also

modelorg, '>optsol, '>optsol_fluxdel, checkOptSol, optimizer and SYBIL_SETTINGS.

Examples

# NOT RUN {
  data(Ec_core)
  Ec_ofd <- oneFluxDel(Ec_core)
# }