Description Details Objects from the Class Slots Extends Methods Author(s) References See Also Examples
The class sysBiolAlg_moma
holds an object of class
optObj
which is generated to meet the
requirements of the MOMA algorithm.
The initialize
method has the following arguments:
An object of class modelorg
.
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
fluxbalance 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
min sum ( (v_j,del  v_j,wt) * sd[j] )^2 for j = 1, ..., n s.t. Sv = 0 a_j <= v_j <= b_j for j = 1, ..., n
with S being the stoichiometric matrix, a_j
and b_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, for j = 1, ..., n).
The total number of variables of the optimization problem is denoted by
n. Here,
v_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
.
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.
Class "sysBiolAlg"
, directly.
No methods defined with class "sysBiolAlg_moma" in the signature.
Gabriel GeliusDietrich <geliudie@uniduesseldorf.de>
Maintainer: Mayo Roettger <mayo.roettger@hhu.de>
Segrè, 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
.
1  showClass("sysBiolAlg_moma")

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