fluxVariability(model, optPercentage, osenseStr, rxnNameList, printLevel, allowLoops, method, cpxControl, advind)¶
Performs flux variablity analysis
Usage[minFlux, maxFlux] = fluxVariability(model, optPercentage, osenseStr, rxnNameList, printLevel, allowLoops, method)
- model – COBRA model structure
- 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
- minFlux – Minimum flux for each reaction
- maxFlux – Maximum flux for each reaction
- 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.
Compares flux ranges by computing the Jaccard index
UsageJ = fvaJaccardIndex(minFlux, maxFlux);
- 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).
- J – An n x 1 vector of Jaccard indices, defined as the intersection divided by the union of all k flux ranges