sysBiolAlg_ccFBA-class: Class `"sysBiolAlg_ccFBA"`

Description

The class sysBiolAlg_ccFBA holds an object of class '>optObj which is generated to meet the requirements of the ccFBA algorithm.

Arguments

Objects from the Class

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.

Slots

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.

Extends

Class "'>sysBiolAlg", directly.

Methods

No methods defined with class "sysBiolAlg_ccFBA" in the signature.

Details

The initialize method has the following arguments:

model: An object of class '>modelorg.
lpdir: Single character string containing the direction of optimization. Can be set to "min" or "max". Default: "max".
LHS: constraint matrix, consists of S matrix and ccFBA constraints
rlb,rub: bounds for constraints (i.e rows)
lb,ub: bounds for variables (i.e columns)
rtype: row constraint type
obj: index of objective
cnames: A character vector giving the variable names. If set to NULL, the reaction id's of model are used. Default: NULL.
rnames: A character vector giving the constraint names. If set to NULL, the metabolite id's of model are used. Default: NULL.
pname: A single character string containing a name for the problem object. Default: NULL.
scaling: Scaling options used to scale the constraint matrix. If set to NULL, no scaling will be performed (see scaleProb). Default: NULL.
writeProbToFileName: 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 $$% \begin{array}{rll}% \max & \mbox{\boldmath$c$\unboldmath}^{\mathrm{T}} \mbox{\boldmath$v$\unboldmath} \\[1ex] \mathrm{s.\,t.} & \mbox{\boldmath$Sv$\unboldmath} = 0 \\[1ex] & \alpha_i \leq v_i \leq \beta_i & \quad \forall i \in \{1, \ldots, n\} \\[1ex] \end{array}% $$ with $\bold{S}$ being the stoichiometric matrix, $\alpha_i$ and $\beta_i$ 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 $ \mbox{\boldmath$c$\unboldmath}^{\mathrm{T}} \mbox{\boldmath$v$\unboldmath} $ under the a given environment and the assumption of steady state. The optimization can be executed by using optimizeProb.

References

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). sybil<U+2013>Efficient constraint-based modelling in R. BMC systems biology, 7(1), 125.