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