mod2irrev: Produces a Model in Irreversible Format

In sybil: Efficient Constrained Based Modelling

Description

The function mod2irrev produces a model with all reactions moving in positive direction.

Usage

  mod2irrev(model, exex = FALSE)

Arguments

model	An object of class modelorg.
exex	Boolean. Exclude exchange fluxes (default: FALSE).

Details

The returned model consists only of reactions moving in positive direction. Reactions with a negative direction in the original model are transferred to positive direction; the corresponding reaction id gets extended by “_r”.

Reversible reactions are split into two reactions. The corresponding reaction ids gets extended by “_f”, or “_b” indicating the original direction.

If exex = TRUE, the exchange reactions were obtained by findExchReact.

Value

An object of class modelorg_irrev.

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.

See Also

modelorg_irrev

Examples

  data(Ec_core)
  Ec_ir <- mod2irrev(Ec_core)

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