fluxVar: Flux Variability Analysis

In sybil: Efficient Constrained Based Modelling

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.

Details

The algorithm is described in sysBiolAlg_fv.

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.

Author(s)

Gabriel Gelius-Dietrich <[e-mail]>

Maintainer: Mayo Roettger <[e-mail]>

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)

Example output

Loading required package: Matrix
Loading required package: lattice
Loading required package: glpkAPI
using GLPK version 4.65
calculating 190 optimizations ... 
|            :            |            :            | 100 %
|===================================================| :-) 
OK
Done.

sybil documentation built on May 31, 2021, 5:08 p.m.