Add Exchange Reactions to a Model
The function addExchReact adds exchange reactions for a set of
metabolites to a metabolic model.
addExchReact(model, met, lb, ub)
model |
An object of class |
met |
A vector of character strings containing the metabolite id's to add exchange reactions for. |
lb |
A vector of numeric values of the same length as |
ub |
A vector of numeric values of the same length as |
If lb[i] < 0, the exchange reaction for the metabolite in met[i]
is considered to be reversible, otherwise irreversible. A reaction id is
generated for each exchange reaction by prepending the metabolite id's with
the string "Ex_".
An object of class modelorg
Gabriel Gelius-Dietrich <geliudie@uni-duesseldorf.de>
Maintainer: Mayo Roettger <mayo.roettger@hhu.de>
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.
# add exchange reactions (allowing input) for the metabolites
# malate and oxalacetate
data(Ec_core)
mod <- addExchReact(Ec_core,
met = c("mal_L[c]", "oaa[c]"),
lb = c(-20, -20))
findExchReact(mod)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.