Files in CausalR

Causal network analysis methods

R/DetermineInteractionTypeOfPath.r R/ComputePValueFromDistributionTable.r R/CreateCG.r R/WriteAllExplainedNodesToSifFile.r R/FindIdsOfConnectedNodesInSubgraph.r R/CalculateSignificanceUsingCubicAlgorithm1b.r R/CausalR-package.r R/GetWeightsFromInteractionInformation.r R/MakePredictionsFromCCG.r R/WriteExplainedNodesToSifFile.r R/ProcessExperimentalData.r R/AnalysePredictionsList.r R/CalculateTotalWeightForAllContingencyTables.r R/GetShortestPathsFromCCG.r R/CreateNetworkFromTable.r R/CreateCCG.r R/GetExplainedNodesOfCCG.r R/FindApproximateValuesThatWillMaximiseDValue.r R/ReadExperimentalData.r R/ValidateFormatOfTable.r R/GetMaxDValueForAFamily.r R/GetMaxDValueForAThreeByTwoFamily.r R/GetScoresWeightsMatrix.r R/AnalyseExperimentalData.r R/GetSetOfDifferentiallyExpressedGenes.r R/GetPathsInSifFormat.r R/GetApproximateMaximumDValueFromTwoByTwoContingencyTable.r R/RankTheHypotheses.r R/ComputeFinalDistribution.r R/PlotGraphWithNodeNames.r R/FindMaximumDValue.r R/PopulateTwoByTwoContingencyTable.r R/RemoveIDsNotInExperimentalData.r R/runSCANR.r R/runRankHypothesis.r R/MakePredictionsFromCG.r R/GetNodeName.r R/GetWeightsAboveHypothesisScoreAndTotalWeights.r R/OrderHypotheses.r R/GetWeightForNumbersOfCorrectandIncorrectPredictions.r R/GetCombinationsOfCorrectandIncorrectPredictions.r R/GetRegulatedNodes.r R/GetInteractionInformation.r R/GetApproximateMaximumDValueFromThreeByTwoContingencyTable.r R/GetScoresWeightsMatrixByCubicAlg.r R/GetMatrixOfCausalRelationships.r R/CheckRowAndColumnSumValuesAreValid.r R/GetScoreForNumbersOfCorrectandIncorrectPredictions.r R/CalculateWeightGivenValuesInThreeByThreeContingencyTable.r R/CalculateSignificanceUsingQuarticAlgorithm.r R/CompareHypothesis.r R/GetRowAndColumnSumValues.r R/CalculateEnrichmentPValue.r R/AddIDsToVertices.r R/AddWeightsToEdges.r R/CheckPossibleValuesAreValid.r R/GetSetOfSignificantPredictions.r R/GetScoresForSingleNode.r R/ValidateFormatOfDataTable.r R/CalculateSignificanceUsingCubicAlgorithm.r R/CalculateSignificance.r R/GetNodeID.r R/GetNumberOfPositiveAndNegativeEntries.r R/GetAllPossibleRoundingCombinations.r R/ReadSifFileToTable.r R/ScoreHypothesis.r R/GetMaximumDValueFromTwoByTwoContingencyTable.r R/GetWeightsAboveHypothesisScoreForAThreeByTwoTable.r R/PopulateTheThreeByThreeContingencyTable.r R/MakePredictions.r vignettes/figure/unnamed-chunk-4-1.pdf vignettes/figure/unnamed-chunk-6-1.pdf man/ReadExperimentalData.Rd man/GetApproximateMaximumDValueFromThreeByTwoContingencyTable.Rd man/CalculateSignificanceUsingQuarticAlgorithm.Rd man/FindIdsOfConnectedNodesInSubgraph.Rd man/DetermineInteractionTypeOfPath.Rd man/GetApproximateMaximumDValueFromTwoByTwoContingencyTable.Rd man/GetNumberOfPositiveAndNegativeEntries.Rd man/GetNodeName.Rd man/ValidateFormatOfDataTable.Rd man/CalculateSignificanceUsingCubicAlgorithm1b.Rd man/GetWeightsAboveHypothesisScoreAndTotalWeights.Rd man/runSCANR.Rd man/GetMaxDValueForAFamily.Rd man/ReadSifFileToTable.Rd man/WriteExplainedNodesToSifFile.Rd man/GetMaximumDValueFromTwoByTwoContingencyTable.Rd man/ProcessExperimentalData.Rd man/ValidateFormatOfTable.Rd man/GetInteractionInformation.Rd man/runRankHypothesis.Rd man/AddIDsToVertices.Rd man/WriteAllExplainedNodesToSifFile.Rd man/PlotGraphWithNodeNames.Rd man/CausalR-package.Rd man/GetAllPossibleRoundingCombinations.Rd man/CheckRowAndColumnSumValuesAreValid.Rd man/MakePredictionsFromCG.Rd man/GetWeightsAboveHypothesisScoreForAThreeByTwoTable.Rd man/GetMaxDValueForAThreeByTwoFamily.Rd man/CalculateSignificanceUsingCubicAlgorithm.Rd man/GetSetOfSignificantPredictions.Rd man/ComputeFinalDistribution.Rd man/MakePredictions.Rd man/GetScoresForSingleNode.Rd man/CalculateSignificance.Rd man/CalculateEnrichmentPValue.Rd man/CreateCCG.Rd man/GetScoreForNumbersOfCorrectandIncorrectPredictions.Rd man/GetMatrixOfCausalRelationships.Rd man/GetWeightsFromInteractionInformation.Rd man/GetNodeID.Rd man/FindMaximumDValue.Rd man/RemoveIDsNotInExperimentalData.Rd man/AnalyseExperimentalData.Rd man/AddWeightsToEdges.Rd man/CreateCG.Rd man/GetSetOfDifferentiallyExpressedGenes.Rd man/GetShortestPathsFromCCG.Rd man/GetWeightForNumbersOfCorrectandIncorrectPredictions.Rd man/PopulateTheThreeByThreeContingencyTable.Rd man/CheckPossibleValuesAreValid.Rd man/CreateNetworkFromTable.Rd man/CalculateTotalWeightForAllContingencyTables.Rd man/GetRowAndColumnSumValues.Rd man/RankTheHypotheses.Rd man/FindApproximateValuesThatWillMaximiseDValue.Rd man/GetCombinationsOfCorrectandIncorrectPredictions.Rd man/GetPathsInSifFormat.Rd man/AnalysePredictionsList.Rd man/GetExplainedNodesOfCCG.Rd man/OrderHypotheses.Rd man/MakePredictionsFromCCG.Rd man/CalculateWeightGivenValuesInThreeByThreeContingencyTable.Rd man/CompareHypothesis.Rd man/GetScoresWeightsMatrixByCubicAlg.Rd man/ScoreHypothesis.Rd man/GetRegulatedNodes.Rd man/ComputePValueFromDistributionTable.Rd man/GetScoresWeightsMatrix.Rd man/PopulateTwoByTwoContingencyTable.Rd tests/runTests.R inst/doc/CausalR.pdf inst/doc/CausalR.R inst/unitTests/DetermineInteractionTypeOfPath.r inst/unitTests/CreateSimpleNetworkForTest_ComputationalCausalGraphCreator.r inst/unitTests/test_EnrichmentPValueCalculation.R inst/unitTests/test_CubicAlgorithm1b.R inst/unitTests/CreateInteractionInfoTableForTest_SifFileReader.r inst/unitTests/test_CubicAlgorithm.R inst/unitTests/test_RankTheHypotheses.R inst/unitTests/test_HypothesisScorer.R inst/unitTests/CreateNetworkForTest_SifFileReader.r inst/unitTests/test_CausalReasoningPredictions.R inst/unitTests/RemoveIDsNotInExperimentalData.r inst/unitTests/test_SifFileReader.R inst/unitTests/test_SignificanceCalculator.R inst/unitTests/GetMatrixOfCausalRelationships.r inst/unitTests/CheckEdgeForTest_SifFileReader.r inst/unitTests/test_QuarticAlgorithm.R inst/unitTests/CreateCGForTest_RankTheHypotheses.r inst/unitTests/CreateTestTableForTest_SifFileReader.r inst/unitTests/test_WriteExplainedNodesToSifFile.R inst/unitTests/test_ExperimentalDataReader.R