findExchReact: Find Exchange Reactions
In sybil: Efficient Constrained Based Modelling

Description Usage Arguments Details Value Author(s) References Examples

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.

1	findExchReact(model)

model

An object of class modelorg, Matrix or matrix.

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.

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.

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.

  data(Ec_core)
  ex  <- findExchReact(Ec_core)
  
  # run FBA
  opt <- optimizeProb(Ec_core)
  
  # get flux distribution of exchange reactions
  getFluxDist(opt, ex)