Description Details Objects from the Class Slots Extends Methods Author(s) References See Also
The class sysBiolAlg_ccFBA
holds an object of class
optObj
which is generated to meet the
requirements of the ccFBA algorithm.
The initialize
method has the following arguments:
An object of class modelorg
.
Single character string containing the direction of optimization.
Can be set to "min"
or "max"
.
Default: "max"
.
constraint matrix, consists of S matrix and ccFBA constraints
bounds for constraints (i.e rows)
bounds for variables (i.e columns)
row constraint type
index of objective
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 cost constraint flux balance analysis (FBA) with a given model, which is basically the solution of a linear programming problem
max c^T v s.t. Sv = 0 a_i <= v_i <= b_i for i = 1, ..., n
with S being the stoichiometric matrix, a_i
and b_i being the lower and upper bounds for flux (variable)
i respectively. The total number of variables of the optimization
problem is denoted by n. The solution of the optimization is a flux
distribution maximizing the objective function
c^T v under the a given environment and the assumption of steady state.
The optimization can be executed by using optimizeProb
.
Objects can be created by calls of the form
sysBiolAlg(model, algorithm = "ccFBA", ...)
.
Arguments to ...
which are passed to method initialize
of class
sysBiolAlg_ccFBA
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_ccFBA" in the signature.
Abdelmoneim Amer Desouki
Adadi, R., Volkmer, B., Milo, R., Heinemann, M., & Shlomi, T. (2012). Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network with Kinetic Parameters, 8(7). doi:10.1371/journal.pcbi.1002575
Gelius-Dietrich, G., Desouki, A. A., Fritzemeier, C. J., & Lercher, M. J. (2013). sybilâ€“Efficient constraint-based modelling in R. BMC systems biology, 7(1), 125.
Constructor function sysBiolAlg
and
superclass sysBiolAlg
.
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