Preparedata

preprocessingOmicsModel(inputData, setMinActiveFlux, setMaxActiveFlux, specificData, TolMaxBoundary)[source]

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)[source]

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