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blockedReact.Rd 2.47 KiB
\name{blockedReact}
\alias{blockedReact}
\title{
Find Blocked Reactions in a Metabolic Network
}
\description{
A blocked Reaction in a metabolic network can not be used by the network,
given the stiochiometric matrix of the network and a set of input and output
fluxes.
}
\usage{
blockedReact(model,
tol = SYBIL_SETTINGS("TOLERANCE"),
exex = TRUE,
fld = FALSE,
retOptSol = FALSE,
verboseMode = 2,
...)
}
\arguments{
\item{model}{
An object of class \code{\link{modelorg}}.
}
\item{tol}{
Tolerance value.\cr
Default: \code{SYBIL_SETTINGS("TOLERANCE")}.
}
\item{exex}{
Boolean, if set to \code{TRUE}, exchange reactions found by
\code{\link{findExchReact}} are excluded from the analysis.\cr
Default: \code{TRUE}.
}
\item{fld}{
Boolean. Save the resulting flux distributions.\cr
Default: \code{FALSE}
}
\item{retOptSol}{
Boolean. Return an object of class
\code{\linkS4class{optsol_blockedReact}} or
just a list containing the results.\cr
Default: \code{FALSE}.
}
\item{verboseMode}{
An integer value indicating the amount of output to stdout:
0: nothing, 1: status messages, 2: like 1 plus a progress indicator.\cr
Default: \code{2}.
}
\item{\dots}{
Further arguments passed to \code{\linkS4class{sysBiolAlg}}.
Argument \code{solverParm} is a good candidate.
}
}
\details{
A reaction \eqn{i} is considered to be \sQuote{blocked}, if its calculated
reaction rate \eqn{v_i}{v[i]} is
\eqn{-\mathrm{tol} < v_i < \mathrm{tol}}{-tol < v[i] < tol}.
Reaction rates are calculated via linear optimization: maximizing and
minimizing each reaction rate. If the difference of the maximum and the
minimum is not larger than \code{tol}, that particular reaction is blocked,
given the current side conditions (exchange fluxes).
}
\value{
If argument \code{retOptsol} is set to \code{TRUE}, an object of class
\code{\linkS4class{optsol_blockedReact}} is returned, otherwise a logical
vector with length equal to the number of reactions of the network. If element
\code{i} equals \code{TRUE}, reaction \code{i} is blocked.
}
\author{
Gabriel Gelius-Dietrich <geliudie@uni-duesseldorf.de>
Maintainer: Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
}
\seealso{
\code{\link{modelorg}},
\code{\linkS4class{optsol_blockedReact}} and
\code{\link{SYBIL_SETTINGS}}.
}
\keyword{optimize}