sybil (version 2.0.0)

sysBiolAlg_room-class: Class "sysBiolAlg_room"

Description

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

Objects from the Class

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.

Slots

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.

Extends

Class "'>sysBiolAlg", directly.

Methods

optimizeProb

signature(object = "sysBiolAlg_room"): runs optimization on the given problem object (see optimizeProb for details).

Details

The initialize method has the following arguments:

model

An object of class '>modelorg.

wtflux

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.

delta

A single numeric value giving the relative range of tolerance, see Details below. Default: 0.03.

epsilon

A single numeric value giving the absolute range of tolerance, see Details below. Default: 0.001.

LPvariant

Boolean. If TRUE, the problem object is formulated as linear program. See Details below. Default: FALSE.

LPvariant

Boolean. If TRUE, the problem object is formulated as linear program. See Details below. Default: FALSE.

absMAX

A single numerical value used as a maximum value for upper variable and contraint bounds. Default: SYBIL_SETTINGS("MAXIMUM").

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 the ROOM algorithm with a given model, which is basically the solution of a mixed integer programming problem $$\text{Unknown environment 'minipage'}$$ with $\text{bold}S$ 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 $ϵ$ specifying absolute and relative ranges in tolerance [Shlomi et al. 2005].

The Boolean argument LPvariant relax the binary contraints to $0\le y_i\le 1$ so that the problem becomes a linear program. The optimization can be executed by using optimizeProb.

References

Shlomi, T., Berkman, O. and Ruppin, E. (2005) Regulatory on/off minimization of metabolic flux changes after genetic pertubations. PNAS 102, 7695--7700.

See Also

Constructor function sysBiolAlg and superclass '>sysBiolAlg.

Examples

# NOT RUN {
  showClass("sysBiolAlg_room")
# }