sybil (version 2.0.0)

fluxVar: Flux Variability Analysis

Description

Performs flux variability analysis for a given model.

Usage

fluxVar(model, react = c(1:react_num(model)), exex = FALSE, ...)

Arguments

model

An object of class '>modelorg.

react

An object of class '>reactId, character or integer. Specifies the fluxes (variables) to analyse. Default: all reactions present in model.

exex

Boolean. Exclude exchange reactions from analysis. If set to TRUE, argument react will be ignored. All reactions present in model will be used, except for the exchange reactions. Default: FALSE

…

Further arguments passed to optimizer. Argument algorithm is set to "fv", further possible arguments are fld, arguments for pre and post processing commands, verboseMode and further arguments passed to the constructor for objects of class '>sysBiolAlg_fv, see there for details.

Value

An object of class '>optsol_fluxVar. The first \(1\) to \(n\) (with \(n\) being the number of elements in argument react) solutions are from the minimizations, and the last \(n+1\) to \(2n\) solutions are from the maximizations.

Details

The algorithm is described in '>sysBiolAlg_fv.

References

Becker, S. A., Feist, A. M., Mo, M. L., Hannum, G., Palsson, B. <U+00D8>. 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. <U+00D8>. (2011) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc 6, 1290--1307.

Bernhard <U+00D8>. Palsson (2006). Systems Biology: Properties of Reconstructed Networks. Cambridge University Press.

Examples

# NOT RUN {
  data(Ec_core)
  fv <- fluxVar(Ec_core)
  plot(fv)
# }