sybil (version 2.2.0)

mod2irrev: Produces a Model in Irreversible Format

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).

Value

An object of class modelorg_irrev.

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.

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.

See Also

'>modelorg_irrev

Examples

# NOT RUN {
  data(Ec_core)
  Ec_ir <- mod2irrev(Ec_core)
# }