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, with fields:

    • .inputData - location or table of the input omics data

    • .activeGenes - genes known to be active

    • .activeReactions - reactions known to be active

    • .inactiveGenes - genes known to be inactive

    • .rxns2add - table of reactions to add to the model

    • .rxns2constrain - table of custom reaction constraints

    • .cellCultureData - cell-culture measurements

    • .mediaData - table of fresh-media constraints

  • 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 reaction Htmi (h[i] -> h[m])

USAGE:

[modelOut, options, problemRxnList, fixedRxnList] = regulariseMitochondrialReactions (model, options, printLevel)

INPUTS:

  • model – COBRA model with fields:

    • .S - m x n stoichiometric matrix

    • .mets - m x 1 metabolite identifiers

    • .rxns - n x 1 reaction identifiers

  • options – structure of context-specific data, with fields:

    • .activeReactions - reactions known to be active (updated when a problem reaction is renamed)

    • .rxns2constrain - table of custom reaction constraints (updated when a problem reaction is renamed)

  • printLevel – set greater than zero to print the old and new reaction formulas

OUTPUTS:

  • modelOut – the input model with h[i] replaced by h[c] in the affected reactions

  • options – the input options structure with reaction identifiers updated

  • problemRxnList – reactions that contained the metabolite h[i]

  • fixedRxnList – the renamed replacement reactions