Select Git revision
oneFluxDel.Rd
Code owners
Assign users and groups as approvers for specific file changes. Learn more.
oneFluxDel.Rd 2.45 KiB
\name{oneFluxDel}
\alias{oneFluxDel}
\encoding{utf8}
\title{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{
\item{model}{
An object of class \code{\linkS4class{modelorg}}.
}
\item{react}{
An object of class \code{\linkS4class{reactId}} or character or integer
containing reaction id's to constrain to zero one by one.\cr
Default: all reactions present in argument \code{model}.
}
\item{lb}{
A numeric vector of the same length as \code{react} containing the lower
bounds for the reaction rates of reactions (variables) given in argument
\code{react}.\cr
Default: \code{0} for all reactions in \code{react}, zero flux through all
reactions.
}
\item{ub}{
A numeric vector of the same length as \code{react} containing the lower
bounds for the reaction rates of reactions (variables) given in argument
\code{react}.\cr
Default: \code{0} for all reactions in \code{react}, zero flux through all
reactions.
}
\item{checkOptSolObj}{
A single logical value. If set to \code{TRUE}, a warning will be generated,
if not all optimizations ended successful.\cr
Default: \code{FALSE}.
}
\item{\dots}{
Further arguments passed to \code{\link{optimizer}}. Important ones are
\code{algorithm} in order to set the algorithm to use or \code{solverParm}
in order to set parameter values for the optimization software.
}
}
\details{
The function \code{oneFluxDel} studies the effect of constraining single
fluxes to zero flux rates on the phenotype of the metabolic network. The
function performs \eqn{n} optimizations with \eqn{n} being the number of
reaction id's given in argument \code{react}. Each optimization corresponds
to the removal of one reaction.
}
\value{
An object of class \code{\linkS4class{optsol_fluxdel}}.
}
\author{
Gabriel Gelius-Dietrich <geliudie@uni-duesseldorf.de>
Maintainer: Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
}
\seealso{
\code{\link{modelorg}}, \code{\linkS4class{optsol}},
\code{\linkS4class{optsol_fluxdel}},
\code{\link{checkOptSol}}, \code{\link{optimizer}} and
\code{\link{SYBIL_SETTINGS}}.
}
\examples{
data(Ec_core)
Ec_ofd <- oneFluxDel(Ec_core)
}
\keyword{optimize}