optimizer: Performs Optimizations for the Gene/Flux Deletion Experiments

Description

This function is used by the gene/flux deletion experiments (the functions oneFluxDel, oneGeneDel, doubleFluxDel and doubleGeneDel) and fills a solution object (a derivative of class optsol) and a problem object depending on the specified solver. The optimizations are then performed by calls to simpleFBA.

Usage

optimizer(model, optsol, lb, ub,
          wtFluxes = NA,
          alg = SYBIL_SETTINGS("ALGORITHM"),
          setToZero = FALSE,
          checkOptSolObj = FALSE,
          rebuildModel = FALSE,
          copyModel = FALSE,
          prCmd = NA, poCmd = NA,
          prDIR = NA, poDIR = NA,
          verboseMode = 3,
          loglevel = -1,
          logfile = NA,
          logfileEnc = NA,
          ...)

Arguments

model

An object of class modelorg.

optsol

An object of a class which inherits class optsol.

A numeric vector containing the lower bounds for the reactions/genes in the dels slot of optsol. If lb is missing, the values are set to 0.

A numeric vector containing the upper bounds for the reactions/genes in the dels slot of optsol. If ub is missing, the values are set to 0.

wtFluxes

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

alg

A single character value. Can be FBA, linearMOMA or linearMOMA_COBRA (see Details below). Default: SYBIL_SETTINGS("ALGORITHM").

setToZero

Logical: If the lp-solver returns a solution which is not optimal, set the corresponding objective value to zero. Default: FALSE.

verboseMode

Single integer value, see sybilLog for possible values. In addition, loglevel > 2 prints a progress bar. Default: 3.

loglevel

Single integer value, see sybilLog for possible values. Default: -1.

logfile

A single character string giving the filename of the logfile. If logfile is set to NA and loglevel is > -1, a default filename is used (see sybilLog

logfileEnc

A single character string giving the encoding for the logfile. If set to NA, the default encoding is used: getOption("encoding"). If logfileEnc is set to something different, the option useFancyQuot

checkOptSolObj

Boolean: check the optsol object with checkOptSol. Default: FALSE.

rebuildModel

Logical. If set to TRUE, the problem object will be rebuilt prior each round of optimization. Default: FALSE.

copyModel

Logical. If set to TRUE, the problem object will be copied from a backup copy of the initial problem object prior each round of optimization. Default: FALSE.

prCmd

A list of preprocessing commands passed to simpleFBA. See there for details. Default: NA.

poCmd

A list of postprocessing commands passed to simpleFBA. See there for details. Default: NA.

prDIR

A numeric or character vector, indicating in which round of optimization the preprocessing command(s) will be executed. prDIR = c(2, 5, 10) executes the commands in prCmd before the second, 5th and 10th optimization. If

poDIR

The same as prDIR, but for postprocessing. Default: NA.

...

Further arguments passed to prepProbObj.

Value

A derivative of class optsol.

encoding

utf8

Details

The function optimizer is called by the functions oneFluxDel, oneGeneDel, doubleFluxDel and doubleGeneDel, but not by a user. The important arguments here are resolve, setToZero, logfile and verboseMode which can be set by using ... in the invoking functions.

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.