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\name{sysBiolAlg_mtf-class}
\Rdversion{1.1}
\encoding{utf8}
\docType{class}
\alias{changeMaxObj,sysBiolAlg_mtf-method}
\alias{changeMaxObj}
\alias{sysBiolAlg_mtf-class}
\alias{sysBiolAlg_mtf}
\alias{mtf}
\title{Class \code{"sysBiolAlg_mtf"}}
\description{
The class \code{sysBiolAlg_mtf} holds an object of class
\code{\linkS4class{optObj}} which is generated to meet the
requirements of the minimize total flux algorithm: minimize the absolute sum
of all fluxes given a previously calculated objective value.
}
\section{Objects from the Class}{
Objects can be created by calls of the form
\code{sysBiolAlg(model, algorithm = "mtf", ...)}.
Arguments to \code{...} which are passed to method \code{initialize} of class
\code{sysBiolAlg_mtf} are described in the Details section.
}
\section{Slots}{
\describe{
\item{\code{maxobj}:}{Object of class \code{"numeric"}
containing optimized objective values.
}
\item{\code{problem}:}{Object of class \code{"optObj"}
containing the problem object.
}
\item{\code{algorithm}:}{Object of class \code{"character"}
containing the name of the algorithm.
}
\item{\code{nr}:}{Object of class \code{"integer"}
containing the number of rows of the problem object.
}
\item{\code{nc}:}{Object of class \code{"integer"}
containing the number of columns of the problem object
}
\item{\code{fldind}:}{Object of class \code{"integer"}
pointers to columns (variables) representing a flux (reaction) in the
original network. The variable \code{fldind[i]} in the problem object
represents reaction \code{i} in the original network.
}
\item{\code{alg_par}:}{Object of class \code{"list"}
containing a named list containing algorithm specific parameters.
}
}
}
\section{Extends}{
Class \code{"\linkS4class{sysBiolAlg}"}, directly.
}
\section{Methods}{
\describe{
\item{changeMaxObj}{\code{signature(object = "sysBiolAlg_mtf")}:
change current objective value to the \eqn{j}th value given in slot
\code{maxobj}. Argument \code{j} must be in \code{[1:length(maxobj)]}.
} }
}
\details{
The \code{initialize} method has the following arguments:
\describe{
\item{model}{
An object of class \code{\linkS4class{modelorg}}.
}
\item{wtobj}{
A single numeric value giving the optimal value. If missing, a default
value is computed based on FBA. If given, arguments \code{solver} and
\code{method} are used, but \code{solverParm} is not.\cr
Default: \code{NULL}.
}
\item{react}{
Arguments \code{react}, \code{lb} and \code{ub} are used, if argument
\code{wtobj} is \code{NULL}, meaning: no previous objective value is
given. Objective values will be calculated via \code{\link{fba}} using
the parameters given in \code{react}, \code{lb} and \code{ub}.\cr
Default: \code{NULL}.
}
\item{lb}{
See argument \code{react}.\cr
Default: \code{NULL}.
}
\item{ub}{
See argument \code{react}.\cr
Default: \code{NULL}.
}
\item{costcoeffw}{
A numeric vector containing cost coefficients for all variables (forward
direction). If set to \code{NULL}, all cost coefficients are set to
\code{1}, so that all variables have the same impact on the objective
function.\cr
Default: \code{NULL}.
}
\item{costcoefbw}{
A numeric vector containing cost coefficients for all variables (backward
direction). If set to \code{NULL}, all cost coefficients are set to the
values given in \code{costcoeffw}.\cr
Default: \code{NULL}.
}
\item{absMAX}{
A single numerical value used as a maximum value for upper variable
and contraint bounds.\cr
Default: \code{SYBIL_SETTINGS("MAXIMUM")}.
}
\item{useNames}{
A single boolean value. If set to \code{TRUE}, variables and constraints
will be named according to \code{cnames} and \code{rnames}. If set to
\code{NULL}, no specific variable or constraint names are set.\cr
Default: \code{SYBIL_SETTINGS("USE_NAMES")}.
}
\item{cnames}{
A character vector giving the variable names. If set to \code{NULL},
the reaction id's of \code{model} are used.\cr
Default: \code{NULL}.
}
\item{rnames}{
A character vector giving the constraint names. If set to \code{NULL},
the metabolite id's of \code{model} are used.\cr
Default: \code{NULL}.
}
\item{pname}{
A single character string containing a name for the problem object.\cr
Default: \code{NULL}.
}
\item{scaling}{
Scaling options used to scale the constraint matrix. If set to \code{NULL}, no scaling will be performed
(see \code{\link{scaleProb}}).\cr
Default: \code{NULL}.
}
\item{writeProbToFileName}{
A single character string containing a file name to which the problem
object will be written in LP file format.\cr
Default: \code{NULL}.
}
\item{...}{
Further arguments passed to the initialize method of
\code{\linkS4class{sysBiolAlg}}. They are \code{solver},
\code{method} and \code{solverParm}.
}
}
The problem object is built to be capable to perform minimize total flux
with a given model, which is basically the solution of a linear programming
problem
\deqn{%
\begin{array}{rll}%
\min & \begin{minipage}[b]{2.5em}
\[
\sum_{i=1}^n cost_i |v_i|
\]
\end{minipage} \\[2em]
\mathrm{s.\,t.} & \mbox{\boldmath$Sv$\unboldmath} = 0 \\[1ex]
& \alpha_i \leq v_i \leq \beta_i
& \quad \forall i \in \{1, \ldots, n\} \\[1ex]
& \mbox{\boldmath$c$\unboldmath}_{\mathrm{wt}} \geq
\mbox{\boldmath$c$\unboldmath}^{\mathrm{T}}
\mbox{\boldmath$v$\unboldmath}_{\mathrm{wt}} \\[1ex]
\end{array}%
}{
min sum cost_i abs(v_i) for i = 1, ..., n
s.t. Sv = 0
a_i <= v_i <= b_i for i = 1, ..., n
c_wt >= c^T v_wt
}
with
\eqn{
\mbox{\boldmath$c$\unboldmath}^{\mathrm{T}}
\mbox{\boldmath$v$\unboldmath}_{\mathrm{wt}}
}{c^T v_wt}
being the previously computed optimized value of the objective function
(argument \code{wtobj}).
The variable \eqn{\bold{S}}{S} denotes the stoichiometric matrix,
\eqn{\alpha_i}{a_i} and \eqn{\beta_i}{b_i} being the lower and upper bounds
for flux (variable) \eqn{i}. The total number of variables of the
optimization problem is denoted by \eqn{n}.
The optimization can be executed by using \code{\link{optimizeProb}}.
}
\references{
Edwards, J. S., Covert, M and Palsson, B. Ø. (2002) Metabolic modelling of
microbes: the flux-balance approach. \emph{Environ Microbiol} \bold{4},
133--140.
Edwards, J. S., Ibarra, R. U. and Palsson, B. Ø. (2001) In silico predictions
of \emph{Escherichia coli} metabolic capabilities are consistent with
experimental data. \emph{Nat Biotechnol} \bold{19}, 125--130.
}
\author{
Gabriel Gelius-Dietrich <geliudie@uni-duesseldorf.de>
Maintainer: Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
}
\seealso{
Constructor function \code{\link{sysBiolAlg}} and
superclass \code{\linkS4class{sysBiolAlg}}.
}
\examples{
showClass("sysBiolAlg_mtf")
}
\keyword{classes}