# 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