"sysBiolAlg_moma"The class sysBiolAlg_moma holds an object of class
'>optObj which is generated to meet the
requirements of the MOMA algorithm.
Objects can be created by calls of the form
sysBiolAlg(model, algorithm = "moma", ...).
Arguments to ... which are passed to method initialize of class
sysBiolAlg_moma are described in the Details section.
problem:Object of class "optObj"
containing the problem object.
algorithm:Object of class "character"
containing the name of the algorithm.
nr:Object of class "integer"
containing the number of rows of the problem object.
nc:Object of class "integer"
containing the number of columns of the problem object
fldind:Object of class "integer"
pointers to columns (variables) representing a flux (reaction) in the
original network. The variable fldind[i] in the problem object
represents reaction i in the original network.
alg_par:Object of class "list"
containing a named list containing algorithm specific parameters.
No methods defined with class "sysBiolAlg_moma" in the signature.
The initialize method has the following arguments:
A numeric vector holding an optimal wild type flux distribution for the
given model. If set to NULL, a default value is computed based on
flux-balance analysis. If given, arguments solver and method
are used, but solverParm is not.
Default: NULL.
A numeric vector or matrix (of class '>Matrix) holding
the quadratic part of the objective function. If set to NULL, a
quadratic unity matrix with number of columns and rows equal to the number
of reactions given in the model is used.
Default: NULL.
A numeric vector containing scaling factors for each reaction in the
objective function. If scaleDist[j] is set to 0, reaction
j will be ignored. The quadratic and the linear part of the
objective function are multiplied by this factor. If set to NULL,
the reactions are not scaled.
Default: NULL.
A single boolean value. If set to TRUE, variables and constraints
will be named according to cnames and rnames. If set to
NULL, no specific variable or constraint names are set.
Default: SYBIL_SETTINGS("USE_NAMES").
A character vector giving the variable names. If set to NULL,
the reaction id's of model are used.
Default: NULL.
A character vector giving the constraint names. If set to NULL,
the metabolite id's of model are used.
Default: NULL.
A single character string containing a name for the problem object.
Default: NULL.
Scaling options used to scale the constraint matrix. If set to
NULL, no scaling will be performed
(see scaleProb).
Default: NULL.
A single character string containing a file name to which the problem
object will be written in LP file format.
Default: NULL.
Further arguments passed to the initialize method of
'>sysBiolAlg. They are solver,
method and solverParm.
The problem object is built to be capable to perform the MOMA algorithm with
a given model, which is basically the solution of a quadratic programming
problem
$$%
\begin{array}{rll}%
\min & \begin{minipage}[b]{5em}
\[
\sum_{j=1}^n
%\bigl(v_{j,\mathrm{del}} - v_{j,\mathrm{wt}}\bigr)^2
\left(\left(v_{j,\mathrm{del}} - v_{j,\mathrm{wt}}\right) \cdot sd_j \right)^2
\]
\end{minipage} \\[2em]
\mathrm{s.\,t.} & \mbox{\boldmath$Sv$\unboldmath} = 0 \\[1ex]
& \alpha_j \leq v_j \leq \beta_j
& \quad \forall j \in \{1, \ldots, n\} \\[1ex]
\end{array}%
$$
with \(\bold{S}\) being the stoichiometric matrix, \(\alpha_j\)
and \(\beta_j\) being the lower and upper bounds for flux (variable)
\(j\) and \(sd_j\) being the scaling factor for reaction \(j\)
(default: \(sd_j = 1,\ \forall j\)).
The total number of variables of the optimization problem is denoted by
\(n\). Here,
\(
\mbox{\boldmath$v$\unboldmath}_{\mathrm{wt}}
\)
is the optimal wild type flux distribution. This can be set via the argument
wtflux. If wtflux is NULL (the default), the
wild type flux distribution will be calculated by a standard FBA.
The optimization can be executed by using optimizeProb.
Segr<U+00E8>, D., Vitkup, D. and Church, G. M. (2002) Analysis or optimality in natural and pertubed metabolic networks. PNAS 99, 15112--15117.
Constructor function sysBiolAlg and
superclass '>sysBiolAlg.
# NOT RUN {
showClass("sysBiolAlg_moma")
# }
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