Modelcreation

createContextSpecificModel(modelPath, trDataPath, mediumDataPath, growthNotAffectingGeneDel, meetMinimumReq, thApproach, lowerTh, upperTh, objective, gmAndOperation, gmOrOperation, constrAll, excludeBiomassEq, biomassId, percentile)[source]

Returns a tissue specific model with parameters provided via graphical intergace of IgemRNA

USAGE

model = deleteInactiveGenes (model, trData, trDataPath, thApproach, lowerTh, upperTh, sheetIndex, growthNotAffectingGeneDel, percentile)

INPUTS

  • modelPath – char full model filename

  • trDataPath – char full transcriptomics data filename

  • mediumDataPath – char full medium data filename

  • growthNotAffectingGeneDel – double (1 or 0) check if grRatio equals 1 after gene deletion compared to wildtype

  • thApproach – double thresholding approach index (1-GT1, 2-LT1, 3-LT2)

  • lowerTh – double lower global threshold value

  • upperTh – double upper global threshold value (required for LT2)

  • objective – char

  • gmAndOperation – char (MIN, GM)

  • gmOrOperation – char (MAX, SUM)

  • constrAll – double (1 or 0)

  • excludeBiomassEq – double (1 or 0)

  • biomassId – char

  • percentile – double (1 or 0) bool option to convert thresholds to percentile value

OUTPUTS

model – extracted model