FVA

fluxVariability(model, optPercentage, osenseStr, rxnNameList, printLevel, allowLoops, method, cpxControl, advind)[source]

Performs flux variablity analysis

Usage

[minFlux, maxFlux] = fluxVariability(model, optPercentage, osenseStr, rxnNameList, printLevel, allowLoops, method)

Input

  • model – COBRA model structure

Optional inputs

  • optPercentage – Only consider solutions that give you at least a certain percentage of the optimal solution (Default = 100 or optimal solutions only)
  • osenseStr – Objective sense (‘min’ or ‘max’) (Default = ‘max’)
  • rxnNameList – List of reactions for which FVA is performed (Default = all reactions in the model)
  • printLevel – Verbose level (default: 0)
  • allowLoops – Whether loops are allowed in solution. (Default = true) See optimizeCbModel for description
  • method – when Vmin and Vmax are in the output, the flux vector can be (Default = 2-norm):
    • ‘FBA’ : standards FBA solution
    • ‘0-norm’ : minimzes the vector 0-norm
    • ‘1-norm’ : minimizes the vector 1-norm
    • ‘2-norm’ : minimizes the vector 2-norm
    • ‘minOrigSol’ : minimizes the euclidean distance of each vector to the original solution vector

cpxControl: solver-specific parameter structure

advind: switch to use the solution basis

  • 0 : default
  • 1 : uses the original problem solution basis as advanced basis

Outputs

  • minFlux – Minimum flux for each reaction
  • maxFlux – Maximum flux for each reaction

Optional outputs

  • Vmin – Matrix of column flux vectors, where each column is a separate minimization.
  • Vmax – Matrix of column flux vectors, where each column is a separate maximization.
fvaJaccardIndex(minFlux, maxFlux)[source]

Compares flux ranges by computing the Jaccard index

Usage

J = fvaJaccardIndex(minFlux, maxFlux);

Inputs

  • minFlux – An n x k matrix of minimum fluxes through n reactions in k different constraint-based models (k > 1).
  • maxFlux – An n x k matrix of maximum fluxes through n reactions in k different constraint-based models (k > 1).

Output

  • J – An n x 1 vector of Jaccard indices, defined as the intersection divided by the union of all k flux ranges