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"calculate overall significance p-value", "concept": [ "CausalR" ], "topics": [ "CalculateSignificance" ] }, { "page": "CalculateSignificanceUsingCubicAlgorithm", "title": "calculate significance using the cubic algorithm", "concept": [ "CausalR" ], "topics": [ "CalculateSignificanceUsingCubicAlgorithm" ] }, { "page": "CalculateSignificanceUsingCubicAlgorithm1b", "title": "Calculate Significance Using Cubic Algorithm", "concept": [ "CausalR" ], "topics": [ "CalculateSignificanceUsingCubicAlgorithm1b" ] }, { "page": "CalculateSignificanceUsingQuarticAlgorithm", "title": "calculate significance using the quartic algorithm", "concept": [ "CausalR" ], "topics": [ "CalculateSignificanceUsingQuarticAlgorithm" ] }, { "page": "CalculateTotalWeightForAllContingencyTables", "title": "calculate total weight for all contingency tables", "topics": [ "CalculateTotalWeightForAllContingencyTables" ] }, { "page": "CalculateWeightGivenValuesInThreeByThreeContingencyTable", "title": "calculate weight given values in three-by-three contingency table", "topics": [ "CalculateWeightGivenValuesInThreeByThreeContingencyTable" ] }, { "page": "CheckPossibleValuesAreValid", "title": "check possible values are valid", "topics": [ "CheckPossibleValuesAreValid" ] }, { "page": "CheckRowAndColumnSumValuesAreValid", "title": "check row and column sum values are valid", "topics": [ "CheckRowAndColumnSumValuesAreValid" ] }, { "page": "CompareHypothesis", "title": "compare hypothesis", "concept": [ "CausalR" ], "topics": [ "CompareHypothesis" ] }, { "page": "ComputeFinalDistribution", "title": "compute final distribution", "topics": [ "ComputeFinalDistribution" ] }, { "page": "ComputePValueFromDistributionTable", "title": "compute a p-value from the distribution table", "topics": [ "ComputePValueFromDistributionTable" ] }, { "page": "CreateCCG", "title": "create a Computational Causal Graph (CCG)", "concept": [ "CausalR" ], "topics": [ "CreateCCG" ] }, { "page": "CreateCG", "title": "create a Computational Graph (CG)", "concept": [ "CausalR" ], "topics": [ "CreateCG" ] }, { "page": "CreateNetworkFromTable", "title": "create network from table", "topics": [ "CreateNetworkFromTable" ] }, { "page": "DetermineInteractionTypeOfPath", "title": "determine interaction type of path", "topics": [ "DetermineInteractionTypeOfPath" ] }, { "page": "FindApproximateValuesThatWillMaximiseDValue", "title": "find approximate values that will maximise D value", "topics": [ "FindApproximateValuesThatWillMaximiseDValue" ] }, { "page": "FindIdsOfConnectedNodesInSubgraph", "title": "find Ids of connected nodes in subgraph", "topics": [ "FindIdsOfConnectedNodesInSubgraph" ] }, { "page": "FindMaximumDValue", "title": "find maximum D value", "topics": [ "FindMaximumDValue" ] }, { "page": "GetAllPossibleRoundingCombinations", "title": "get score for numbers of correct and incorrect predictions", "topics": [ "GetAllPossibleRoundingCombinations" ] }, { "page": "GetApproximateMaximumDValueFromThreeByTwoContingencyTable", "title": "returns approximate maximum D value or weight for a 3x2 superfamily", "topics": [ "GetApproximateMaximumDValueFromThreeByTwoContingencyTable" ] }, { "page": "GetApproximateMaximumDValueFromTwoByTwoContingencyTable", "title": "computes an approximate maximum D value or weight", "topics": [ "GetApproximateMaximumDValueFromTwoByTwoContingencyTable" ] }, { "page": "GetCombinationsOfCorrectandIncorrectPredictions", "title": "returns table of correct and incorrect predictions", "topics": [ "GetCombinationsOfCorrectandIncorrectPredictions" ] }, { "page": "GetExplainedNodesOfCCG", "title": "Get explained nodes of CCG", "topics": [ "GetExplainedNodesOfCCG" ] }, { "page": "GetInteractionInformation", "title": "returns interaction information from input data", "topics": [ "GetInteractionInformation" ] }, { "page": "GetMatrixOfCausalRelationships", "title": "compute causal relationships matrix", "topics": [ "GetMatrixOfCausalRelationships" ] }, { "page": "GetMaxDValueForAFamily", "title": "get maximun D value for a family", "topics": [ "GetMaxDValueForAFamily" ] }, { "page": "GetMaxDValueForAThreeByTwoFamily", "title": "get maximum D value for three-by-two a family", "topics": [ "GetMaxDValueForAThreeByTwoFamily" ] }, { "page": "GetMaximumDValueFromTwoByTwoContingencyTable", "title": "get maximum D value from two-by-two contingency table", "topics": [ "GetMaximumDValueFromTwoByTwoContingencyTable" ] }, { "page": "GetNodeID", "title": "get CCG node ID", "topics": [ "GetNodeID" ] }, { "page": "GetNodeName", "title": "get node name", "concept": [ "CausalR" ], "topics": [ "GetNodeName" ] }, { "page": "GetNumberOfPositiveAndNegativeEntries", "title": "counts the number of positive and negative entries", "concept": [ "CausalR" ], "topics": [ "GetNumberOfPositiveAndNegativeEntries" ] }, { "page": "GetPathsInSifFormat", "title": "Get paths in Sif format", "topics": [ "GetPathsInSifFormat" ] }, { "page": "GetRegulatedNodes", "title": "get regulated nodes", "topics": [ "GetRegulatedNodes" ] }, { "page": "GetRowAndColumnSumValues", "title": "get row and column sum values", "topics": [ "GetRowAndColumnSumValues" ] }, { "page": "GetScoreForNumbersOfCorrectandIncorrectPredictions", "title": "returns the score for a given number of correct and incorrect predictions", "topics": [ "GetScoreForNumbersOfCorrectandIncorrectPredictions" ] }, { "page": "GetScoresForSingleNode", "title": "Get scores for single node", "topics": [ "GetScoresForSingleNode" ] }, { "page": "GetScoresWeightsMatrix", "title": "get scores weight matrix", "topics": [ "GetScoresWeightsMatrix" ] }, { "page": "GetScoresWeightsMatrixByCubicAlg", "title": "get scores weights matrix by the cubic algorithm", "topics": [ "GetScoresWeightsMatrixByCubicAlg" ] }, { "page": "GetSetOfDifferentiallyExpressedGenes", "title": "get set of differientially expressed genes", "topics": [ "GetSetOfDifferentiallyExpressedGenes" ] }, { "page": "GetSetOfSignificantPredictions", "title": "get set of significant predictions", "topics": [ "GetSetOfSignificantPredictions" ] }, { "page": "GetShortestPathsFromCCG", "title": "get shortest paths from CCG", "concept": [ "CausalR" ], "topics": [ "GetShortestPathsFromCCG" ] }, { "page": "GetWeightForNumbersOfCorrectandIncorrectPredictions", "title": "get weight for numbers of correct and incorrect predictions", "topics": [ "GetWeightForNumbersOfCorrectandIncorrectPredictions" ] }, { "page": "GetWeightsAboveHypothesisScoreAndTotalWeights", "title": "get weights above hypothesis score and total weights", "topics": [ "GetWeightsAboveHypothesisScoreAndTotalWeights" ] }, { "page": "GetWeightsAboveHypothesisScoreForAThreeByTwoTable", "title": "updates weights for contingency table and produce values for p-value calculation", "topics": [ "GetWeightsAboveHypothesisScoreForAThreeByTwoTable" ] }, { "page": "GetWeightsFromInteractionInformation", "title": "get weights from interaction information", "topics": [ "GetWeightsFromInteractionInformation" ] }, { "page": "MakePredictions", "title": "make predictions", "concept": [ "CausalR" ], "topics": [ "MakePredictions" ] }, { "page": "MakePredictionsFromCCG", "title": "make predictions from CCG", "concept": [ "CausalR" ], "topics": [ "MakePredictionsFromCCG" ] }, { "page": "MakePredictionsFromCG", "title": "make predictions from CG", "concept": [ "CausalR" ], "topics": [ "MakePredictionsFromCG" ] }, { "page": "OrderHypotheses", "title": "order hypotheses", "topics": [ "OrderHypotheses" ] }, { "page": "PlotGraphWithNodeNames", "title": "plot graph with node names", "concept": [ "CausalR" ], "topics": [ "PlotGraphWithNodeNames" ] }, { "page": "PopulateTheThreeByThreeContingencyTable", "title": "populate the three-by-three contingency table", "topics": [ "PopulateTheThreeByThreeContingencyTable" ] }, { "page": "PopulateTwoByTwoContingencyTable", "title": "Populate Two by Two Contingency Table", "topics": [ 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