sybil (version 1.1.2)

findExchReact: Find Exchange Reactions

Description

This function identifies reactions in a metabolic network which transport metabolites accross the network boundary. Only the stroichiometric matrix is taken into account, so the identified reactions are basically those, having only one non-zero entry in their column of the stroichiometric matrix. In order to work, the network must be open, it must not contain boundary metabolites.

Usage

findExchReact(model)

Arguments

model

An object of class modelorg, Matrix or matrix.

Value

• If model is of class modelorg a list is returned:
• exchange
  An object of class reactId containing the id's of the exchange fluxes.
• uptake
  An integer vector giving the index of uptake reactions react_id(model)[x$uptake] has the reaction id's of the uptake reactions.
• metabolite
  An integer vector giving the index of metabolite id's in met_id(model) having an exchange reaction.
• Otherwise, if model is of class matrix or of class Matrix, a logical vector is returned. If element i equals TRUE, column i of model is an exchange reaction.

encoding

utf8

Details

A exchange reaction $j$ for a particular metabolite $i$ has exactly one non-zero entry in the stoichiometric matrix $S_{ij} \in {-1, 1}$. If $S_{ij} = -1$, reaction $j$ is considered to be an uptake (source) reaction.

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.

Examples

data(Ec_core)
  ex <- findExchReact(Ec_core)