sybil (version 1.1.2)

fluxVar: Flux Variability Analysis

Description

Performs flux variablilty analysis for a given model.

Usage

fluxVar(model, react, fld = FALSE, verboseMode = 2, ...)

Arguments

model

An object of class modelorg.

react

An object of class reactId, character or integer. Specifies the fluxes (variables) to analyse. If left empty: react_id(model).

fld

Boolean. Save the resulting flux distribution. Default: FALSE

verboseMode

An integer value indicating the amount of output to stdout: 0: nothing, 1: status messages, 2: like 1 plus a progress indicator, 3: a table containing the reaction id's and the corresponding min max values. Default: 2.

...

Further arguments passed to sysBiolAlg. See class sysBiolAlg_fv for details.

Value

• An object of class optsol_fluxVar.

encoding

utf8

Details

The algorithm is described in sysBiolAlg_fv.

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.

Bernhard Ø. Palsson (2006). Systems Biology: Properties of Reconstructed Networks. Cambridge University Press.

Examples

data(Ec_core)
  fv <- fluxVar(Ec_core)
  plot(fv)