sysBiolAlg_moma-class: Class '"sysBiolAlg_moma"'

In sybil: Efficient Constrained Based Modelling

Description

The class sysBiolAlg_moma holds an object of class optObj which is generated to meet the requirements of the MOMA algorithm.

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 set to NULL, a default value is computed based on flux-balance analysis. If given, arguments solver and method are used, but solverParm is not. Default: NULL.

Qmat

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.

scaleDist

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.

useNames

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").

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 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 from the Class

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.

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_moma" in the signature.

Author(s)

Gabriel Gelius-Dietrich <[e-mail]>

Maintainer: Mayo Roettger <[e-mail]>

References

Segrè, D., Vitkup, D. and Church, G. M. (2002) Analysis or optimality in natural and pertubed metabolic networks. PNAS 99, 15112–15117.

See Also

Constructor function sysBiolAlg and superclass sysBiolAlg.

Examples

  showClass("sysBiolAlg_moma")

sybil documentation built on May 31, 2021, 5:08 p.m.