prepProbObj: Creates an Instance of Class "optObj"

Description

The function prepProbObj creates an instance of class optObj with respect to the specified solver.

Usage

prepProbObj(model, nCols, nRows,
              wtflux = NA,
              MOMAflag = FALSE,
              COBRAflag = FALSE,
              minTotalFluxFLAG = FALSE,
              minDistFLAG = FALSE,
              scaling = NA,
              solver = SYBIL_SETTINGS("SOLVER"),
              method = SYBIL_SETTINGS("METHOD"),
              lpdir = SYBIL_SETTINGS("OPT_DIRECTION"),
              solverParm = SYBIL_SETTINGS("SOLVER_CTRL_PARM"))

Arguments

model

An object of class modelorg.

nCols

Number of columns (variables) of the problem object.

nRows

Number of rows (constraints) of the problem object.

wtflux

A single numeric value, or a numeric vector of length equal to the number of fluxes (variables) in the model (see simpleFBA). Default: NA.

MOMAflag

Boolean, prepare problem object in order to perform minimization of metabolic adjustment (MOMA, see optimizer). Default: FALSE.

COBRAflag

Boolean, prepare problem object in order to perform minimization of metabolic adjustment as in COBRA (MOMA, see optimizer). Default: FALSE.

minTotalFluxFLAG

Boolean, prepare problem object in order to find a flux distribution with minimal total flux leading to an optimal value for the objective function (see simpleFBA). Default: FALSE.

minDistFLAG

Boolean, prepare problem object in order to find a flux distribution with a minimal manhattan distance to a given flux (see simpleFBA). Default: FALSE.

scaling

Scaling options used to scale the constraint matrix. If set to NA, no scaling will be performed (see optObj). Default: FALSE.

solver

Single character value. The solver to use. See SYBIL_SETTINGS for possible values. Default: SYBIL_SETTINGS("SOLVER").

method

Single character value. The optimization algorithm to use. Possible values depend on the setting in solver. See SYBIL_SETTINGS for possible values. Default: SYBIL_SETTIN

lpdir

Character value, direction of optimisation. Can be set to "min" or "max". Default: SYBIL_SETTINGS("OPT_DIRECTION").

solverParm

A data frame containing parameters for the specified solver. Default: SYBIL_SETTINGS("SOLVER_CTRL_PARM"), (see Details below).

Value

An object of class optObj, or FALSE.

encoding

utf8

Details

The function prepProbObj creates an instance of class optObj with respect to the specified solver and desired algorithm. The object type (slot oobj) is determined by the argument solver. The properties of the problem itself are dependent on the specified algorithm (e.g. number of rows and columns of the constraint matrix, etc.). Parameters can be set as data frame: solverParm = data.frame(parm1 = val1, parm2 = val2) with parm1 and parm2 beeing the names of two different parameters and val1 and val2 the corresponding values. For possible parameters and values see the documentation of the used solver package (e.g. glpkAPI).

References

Becker, S. A., Feist, A. M., Mo, M. L., Hannum, G., Palsson, B. Ø. and Herrgard, M. J. (2007) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat Protoc 2, 727--738.

Schellenberger, J., Que, R., Fleming, R. M. T., Thiele, I., Orth, J. D., Feist, A. M., Zielinski, D. C., Bordbar, A., Lewis, N. E., Rahmanian, S., Kang, J., Hyduke, D. R. and Palsson, B. Ø. (2011) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc 6, 1290--1307.