Preparedata

preprocessingOmicsModel(inputData, setMinActiveFlux, setMaxActiveFlux, specificData, TolMaxBoundary)

Prepare data for the omicsModelGeneration function

USAGE:

specificData = preprocessingOmicsModel (inputData)

INPUT:

inputData – Location of the file containing the optional variables where the first row of each column represents the name of the optional variables and the following rows represent the data on them.

OPTIONAL INPUT:

• setMinActiveFlux {0}, 1 - change the LB of forced – active reactions based on the (primal) feasibility tolerance (feasTol*100)

• setMaxActiveFlux {0}, 1 - change the UB of forced – active reactions based on the (primal) feasibility

  tolerance (based on param.TolMaxBoundary, feasTol*1e9 if not provided)

  specificData: Structure containing the optional variables to

  generate a context-specific omics model

  TolMaxBoundary: The reaction boundary’s maximum value (Default: feasTol*1e9).

OUTPUT:

specificData – Structure containing the additional optional variables to generate a context-specific omics model

regulariseMitochondrialReactions(model, options, printLevel)

replace the metabolite h[i] with h[c] and remove the rection Htmi h[i] -> h[m]