"sysBiolAlg_room"The class sysBiolAlg_room holds an object of class
'>optObj which is generated to meet the
requirements of the ROOM algorithm.
Objects can be created by calls of the form
sysBiolAlg(model, algorithm = "room", ...).
Arguments to ... which are passed to method initialize of class
sysBiolAlg_room are described in the Details section.
wu:Object of class "numeric"
containing the upper threshold for a significant flux change,
see Details below.
wl:Object of class "numeric"
containing the lower threshold for a significant flux change,
see Details below.
fnc:Object of class "integer"
containing the number of reactions in the entire metabolic network
(argument model to the constructor function
sysBiolAlg).
fnr:Object of class "integer"
containing the number of metabolites in the entire metabolic network
(argument model to the constructor function
sysBiolAlg).
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.
signature(object = "sysBiolAlg_room"):
runs optimization on the given problem object
(see optimizeProb for details).
The initialize method has the following arguments:
A numeric vector holding an optimal wild type flux distribution for the
given model. If missing, a default value is computed based on FBA.
If given, arguments solver and method are used to calculate
the dafault, but solverParm is not.
A single numeric value giving the relative range of tolerance, see
Details below.
Default: 0.03.
A single numeric value giving the absolute range of tolerance, see
Details below.
Default: 0.001.
Boolean. If TRUE, the problem object is formulated as linear
program. See Details below.
Default: FALSE.
Boolean. If TRUE, the problem object is formulated as linear
program. See Details below.
Default: FALSE.
A single numerical value used as a maximum value for upper variable
and contraint bounds.
Default: SYBIL_SETTINGS("MAXIMUM").
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 ROOM algorithm with
a given model, which is basically the solution of a mixed integer programming
problem
$$%
\begin{array}{rll}%
\min & \begin{minipage}[b]{5em}
\[
\sum_{i=1}^n y_i
\]
\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]
& v_i - y(\beta_i - w_i^u) \leq w_i^u \\[1ex]
& v_i - y(\alpha_i - w_i^l) \geq w_i^l \\[1ex]
& y_i \in \{0, 1\} \\[1ex]
& w_i^u = w_i + \delta |w_i| + \epsilon \\[1ex]
& w_i^l = w_i - \delta |w_i| - \epsilon \\[1ex]
\end{array}%
$$
with \(\bold{S}\) being the stoichiometric matrix, \(\alpha_i\)
and \(\beta_i\) being the lower and upper bounds for flux (variable)
\(i\).
The total number of fluxes of the optimization problem is denoted by \(n\).
Here, \(w\) 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.
All variables \(y_i\) are binary, with \(y_i = 1\) for a significant flux
change in \(v_i\) and \(y_i = 0\) otherwise. Thresholds determining the
significance of a flux change are given in \(w^u\) and \(w^l\), with
\(\delta\) and \(\epsilon\) specifying absolute and
relative ranges in tolerance [Shlomi et al. 2005].
The Boolean argument LPvariant relax the binary contraints to
\(0 \leq y_i \leq 1\) so that the problem becomes a linear
program.
The optimization can be executed by using optimizeProb.
Shlomi, T., Berkman, O. and Ruppin, E. (2005) Regulatory on/off minimization of metabolic flux changes after genetic pertubations. PNAS 102, 7695--7700.
Constructor function sysBiolAlg and
superclass '>sysBiolAlg.
# NOT RUN {
showClass("sysBiolAlg_room")
# }
Run the code above in your browser using DataLab