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 optimizeProb.

Usage

optimizer(model, lb, ub,
          delete, geneFlag,
          alg = SYBIL_SETTINGS("ALGORITHM"),
          setToZero = FALSE,
          checkOptSolObj = FALSE,
          rebuildModel = FALSE,
          fld = "none",
          prCmd = NA, poCmd = NA,
          prDIR = NA, poDIR = NA,
          verboseMode = 2,
          ...)

Arguments

model

An object of class modelorg.

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.

delete

A matrix containing gene id's or indices of fluxes to delete. The deletions were performed line by line.

geneFlag

A boolean flag. If set to TRUE, all entries in delete are considered to be gene id's, otherwise, they were treated as fluxes.

fld

Type of flux distribution to return. If set to "none", no flux distribution will be returned. If set to "fluxes", only the real flux distribution is returned, meaning all variable values after optimization representin

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, giving the amount of output to the console. Use sink to redirect output to a file. If loglevel == 2, a progress bar will be produced. If loglevel > 2, in

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.

prCmd

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

poCmd

A list of postprocessing commands passed to optimizeProb. 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 sysBiolAlg.

Value

A derivative of class optsol.

encoding

utf8

Details

The function optimizer is called by the functions oneFluxDel, oneGeneDel, doubleFluxDel, doubleGeneDel and geneDeletion, but not directly by a user. The function optimizer runs a series of optimizations, whereas the function optimizeProb only runs exactly one optimization. In principle, optimizer is a kind of wrapper to optimizeProb.

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.