Inactivegenedeletion

deleteInactiveGenes(model, trData, trDataPath, thApproach, lowerTh, upperTh, sheetIndex, growthNotAffectingGeneDel, percentile)[source]

Returns a tissue specific model with inactive genes deleted

USAGE:

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

INPUTS:

  • model – COBRA model structure with fields:

    • .genes - gene identifiers checked against the inactive-gene list

  • trData – table with columns ‘GeneId’ and ‘Data’, with fields:

    • .Data - gene expression values

    • .Geneid - gene identifiers

  • trDataPath – char full transcriptomics data filename

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

  • lowerTh – double

  • upperTh – double (required for LT2)

  • sheetIndex – double transcriptomics dataset sheet index

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

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

OUTPUTS:

model – extracted model