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| CausalR-package | The CausalR package |
| AddIDsToVertices | add IDs to vertices |
| AddWeightsToEdges | add weights to edges |
| AnalyseExperimentalData | analyse experimental data |
| AnalysePredictionsList | analyse predictions list |
| CalculateEnrichmentPValue | calculates an enrichment p-value |
| CalculateSignificance | calculate overall significance p-value |
| CalculateSignificanceUsingCubicAlgorithm | calculate significance using the cubic algorithm |
| CalculateSignificanceUsingCubicAlgorithm1b | Calculate Significance Using Cubic Algorithm |
| CalculateSignificanceUsingQuarticAlgorithm | calculate significance using the quartic algorithm |
| CalculateTotalWeightForAllContingencyTables | calculate total weight for all contingency tables |
| CalculateWeightGivenValuesInThreeByThreeContingencyTable | calculate weight given values in three-by-three contingency table |
| CausalR | The CausalR package |
| CheckPossibleValuesAreValid | check possible values are valid |
| CheckRowAndColumnSumValuesAreValid | check row and column sum values are valid |
| CompareHypothesis | compare hypothesis |
| ComputeFinalDistribution | compute final distribution |
| ComputePValueFromDistributionTable | compute a p-value from the distribution table |
| CreateCCG | create a Computational Causal Graph (CCG) |
| CreateCG | create a Computational Graph (CG) |
| CreateNetworkFromTable | create network from table |
| DetermineInteractionTypeOfPath | determine interaction type of path |
| FindApproximateValuesThatWillMaximiseDValue | find approximate values that will maximise D value |
| FindIdsOfConnectedNodesInSubgraph | find Ids of connected nodes in subgraph |
| FindMaximumDValue | find maximum D value |
| GetAllPossibleRoundingCombinations | get score for numbers of correct and incorrect predictions |
| GetApproximateMaximumDValueFromThreeByTwoContingencyTable | returns approximate maximum D value or weight for a 3x2 superfamily |
| GetApproximateMaximumDValueFromTwoByTwoContingencyTable | computes an approximate maximum D value or weight |
| GetCombinationsOfCorrectandIncorrectPredictions | returns table of correct and incorrect predictions |
| GetExplainedNodesOfCCG | Get explained nodes of CCG |
| GetInteractionInformation | returns interaction information from input data |
| GetMatrixOfCausalRelationships | compute causal relationships matrix |
| GetMaxDValueForAFamily | get maximun D value for a family |
| GetMaxDValueForAThreeByTwoFamily | get maximum D value for three-by-two a family |
| GetMaximumDValueFromTwoByTwoContingencyTable | get maximum D value from two-by-two contingency table |
| GetNodeID | get CCG node ID |
| GetNodeName | get node name |
| GetNumberOfPositiveAndNegativeEntries | counts the number of positive and negative entries |
| GetPathsInSifFormat | Get paths in Sif format |
| GetRegulatedNodes | get regulated nodes |
| GetRowAndColumnSumValues | get row and column sum values |
| GetScoreForNumbersOfCorrectandIncorrectPredictions | returns the score for a given number of correct and incorrect predictions |
| GetScoresForSingleNode | Get scores for single node |
| GetScoresWeightsMatrix | get scores weight matrix |
| GetScoresWeightsMatrixByCubicAlg | get scores weights matrix by the cubic algorithm |
| GetSetOfDifferentiallyExpressedGenes | get set of differientially expressed genes |
| GetSetOfSignificantPredictions | get set of significant predictions |
| GetShortestPathsFromCCG | get shortest paths from CCG |
| GetWeightForNumbersOfCorrectandIncorrectPredictions | get weight for numbers of correct and incorrect predictions |
| GetWeightsAboveHypothesisScoreAndTotalWeights | get weights above hypothesis score and total weights |
| GetWeightsAboveHypothesisScoreForAThreeByTwoTable | updates weights for contingency table and produce values for p-value calculation |
| GetWeightsFromInteractionInformation | get weights from interaction information |
| MakePredictions | make predictions |
| MakePredictionsFromCCG | make predictions from CCG |
| MakePredictionsFromCG | make predictions from CG |
| OrderHypotheses | order hypotheses |
| PlotGraphWithNodeNames | plot graph with node names |
| PopulateTheThreeByThreeContingencyTable | populate the three-by-three contingency table |
| PopulateTwoByTwoContingencyTable | Populate Two by Two Contingency Table |
| ProcessExperimentalData | process experimental data |
| RankTheHypotheses | rank the hypotheses |
| ReadExperimentalData | read experimental data |
| ReadSifFileToTable | read .sif to Table |
| RemoveIDsNotInExperimentalData | remove IDs not in experimental data |
| runRankHypothesis | run rank the hypothesis |
| runSCANR | run ScanR |
| ScoreHypothesis | score hypothesis |
| ValidateFormatOfDataTable | validate format of the experimental data table |
| ValidateFormatOfTable | validate format of table |
| WriteAllExplainedNodesToSifFile | Write all explained nodes to Sif file |
| WriteExplainedNodesToSifFile | Write explained nodes to Sif file |