sybil (version 2.0.0)

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 an object of class '>reactId_Exch is returned. 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. The function returns NULL and gives a warning, if no exchange reaction can be found.

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. <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.

Examples

# NOT RUN {
  data(Ec_core)
  ex  <- findExchReact(Ec_core)
  
  # run FBA
  opt <- optimizeProb(Ec_core)
  
  # get flux distribution of exchange reactions
  getFluxDist(opt, ex)
# }