sysBiolAlg_mtf-class: Class '"sysBiolAlg_mtf"'

In sybil: Efficient Constrained Based Modelling

Description

The class sysBiolAlg_mtf holds an object of class optObj which is generated to meet the requirements of the minimize total flux algorithm: minimize the absolute sum of all fluxes given a previously calculated objective value.

Details

The initialize method has the following arguments:

model

An object of class modelorg.

wtobj

A single numeric value giving the optimal value. If missing, a default value is computed based on FBA. If given, arguments solver and method are used, but solverParm is not.
Default: NULL.

react

Arguments react, lb and ub are used, if argument wtobj is NULL, meaning: no previous objective value is given. Objective values will be calculated via fba using the parameters given in react, lb and ub.
Default: NULL.

lb

See argument react.
Default: NULL.

ub

See argument react.
Default: NULL.

costcoeffw

A numeric vector containing cost coefficients for all variables (forward direction). If set to NULL, all cost coefficients are set to 1, so that all variables have the same impact on the objective function.
Default: NULL.

costcoefbw

A numeric vector containing cost coefficients for all variables (backward direction). If set to NULL, all cost coefficients are set to the values given in costcoeffw.
Default: NULL.

absMAX

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

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 minimize total flux with a given model, which is basically the solution of a linear programming problem

min sum cost_i abs(v_i) for i = 1, ..., n s.t. Sv = 0 a_i <= v_i <= b_i for i = 1, ..., n c_wt >= c^T v_wt

with c^T v_wt being the previously computed optimized value of the objective function (argument wtobj). The variable S denotes the stoichiometric matrix, a_i and b_i being the lower and upper bounds for flux (variable) i. The total number of variables of the optimization problem is denoted by n. The optimization can be executed by using optimizeProb.

Objects from the Class

Objects can be created by calls of the form

sysBiolAlg(model, algorithm = "mtf", ...).

Arguments to ... which are passed to method initialize of class sysBiolAlg_mtf are described in the Details section.

Slots

maxobj:

Object of class "numeric" containing optimized objective values.

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

changeMaxObj

signature(object = "sysBiolAlg_mtf"): change current objective value to the jth value given in slot maxobj. Argument j must be in [1:length(maxobj)].

Author(s)

Gabriel Gelius-Dietrich <[e-mail]>

Maintainer: Mayo Roettger <[e-mail]>

References

Edwards, J. S., Covert, M and Palsson, B. Ø. (2002) Metabolic modelling of microbes: the flux-balance approach. Environ Microbiol 4, 133–140.

Edwards, J. S., Ibarra, R. U. and Palsson, B. Ø. (2001) In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol 19, 125–130.

See Also

Constructor function sysBiolAlg and superclass sysBiolAlg.

Examples

  showClass("sysBiolAlg_mtf")

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