sybil (version 1.0.2)

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.

encoding

utf8

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. 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)