CausalR: Causal Reasoning Methods

Causal reasoning methods for biological networks, to enable regulator prediction and reconstruction of regulatory networks from high dimensional data.

AuthorGlyn Bradley, Steven Barrett, David Wiley, Bhushan Bonde, Peter Woollard, Chirag Mistry, David Riley, Mark Pipe
Date of publicationNone
MaintainerGlyn Bradley <glyn.x.bradley@gsk.com>, Steven Barrett <steven.j.barrett@gsk.com>, Bhushan Bonde <bkbonde@gmail.com>
LicenseGPL (>= 2)
Version1.6.0

View on Bioconductor

Man pages

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...

CausalR-package: 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...

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...

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...

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

WriteExplainedNodesToSifFile: Write explained nodes to Sif file

Functions

AddIDsToVertices Man page
AddWeightsToEdges Man page
AnalyseExperimentalData Man page
AnalysePredictionsList Man page
CalculateEnrichmentPValue Man page
CalculateSignificance Man page
CalculateSignificanceUsingCubicAlgorithm Man page
CalculateSignificanceUsingCubicAlgorithm1b Man page
CalculateSignificanceUsingQuarticAlgorithm Man page
CalculateTotalWeightForAllContingencyTables Man page
CalculateWeightGivenValuesInThreeByThreeContingencyTable Man page
CausalR Man page
CausalR-package Man page
CheckPossibleValuesAreValid Man page
CheckRowAndColumnSumValuesAreValid Man page
CompareHypothesis Man page
ComputeFinalDistribution Man page
ComputePValueFromDistributionTable Man page
CreateCCG Man page
CreateCG Man page
CreateNetworkFromTable Man page
DetermineInteractionTypeOfPath Man page
FindApproximateValuesThatWillMaximiseDValue Man page
FindIdsOfConnectedNodesInSubgraph Man page
FindMaximumDValue Man page
GetAllPossibleRoundingCombinations Man page
GetApproximateMaximumDValueFromThreeByTwoContingencyTable Man page
GetApproximateMaximumDValueFromTwoByTwoContingencyTable Man page
GetCombinationsOfCorrectandIncorrectPredictions Man page
GetExplainedNodesOfCCG Man page
GetInteractionInformation Man page
GetMatrixOfCausalRelationships Man page
GetMaxDValueForAFamily Man page
GetMaxDValueForAThreeByTwoFamily Man page
GetMaximumDValueFromTwoByTwoContingencyTable Man page
GetNodeID Man page
GetNodeName Man page
GetNumberOfPositiveAndNegativeEntries Man page
GetPathsInSifFormat Man page
GetRegulatedNodes Man page
GetRowAndColumnSumValues Man page
GetScoreForNumbersOfCorrectandIncorrectPredictions Man page
GetScoresForSingleNode Man page
GetScoresWeightsMatrix Man page
GetScoresWeightsMatrixByCubicAlg Man page
GetSetOfDifferentiallyExpressedGenes Man page
GetSetOfSignificantPredictions Man page
GetShortestPathsFromCCG Man page
GetWeightForNumbersOfCorrectandIncorrectPredictions Man page
GetWeightsAboveHypothesisScoreAndTotalWeights Man page
GetWeightsAboveHypothesisScoreForAThreeByTwoTable Man page
GetWeightsFromInteractionInformation Man page
MakePredictions Man page
MakePredictionsFromCCG Man page
MakePredictionsFromCG Man page
OrderHypotheses Man page
PlotGraphWithNodeNames Man page
PopulateTheThreeByThreeContingencyTable Man page
PopulateTwoByTwoContingencyTable Man page
ProcessExperimentalData Man page
RankTheHypotheses Man page
ReadExperimentalData Man page
ReadSifFileToTable Man page
RemoveIDsNotInExperimentalData Man page
runRankHypothesis Man page
runSCANR Man page
ScoreHypothesis Man page
ValidateFormatOfDataTable Man page
ValidateFormatOfTable Man page
WriteExplainedNodesToSifFile Man page

Files

CausalR/DESCRIPTION
CausalR/NAMESPACE
CausalR/R
CausalR/R/AddIDsToVertices.r
CausalR/R/AddWeightsToEdges.r
CausalR/R/AnalyseExperimentalData.r
CausalR/R/AnalysePredictionsList.r
CausalR/R/CalculateEnrichmentPValue.r
CausalR/R/CalculateSignificance.r
CausalR/R/CalculateSignificanceUsingCubicAlgorithm.r
CausalR/R/CalculateSignificanceUsingCubicAlgorithm1b.r
CausalR/R/CalculateSignificanceUsingQuarticAlgorithm.r
CausalR/R/CalculateTotalWeightForAllContingencyTables.r
CausalR/R/CalculateWeightGivenValuesInThreeByThreeContingencyTable.r
CausalR/R/CausalR-package.r
CausalR/R/CheckPossibleValuesAreValid.r
CausalR/R/CheckRowAndColumnSumValuesAreValid.r
CausalR/R/CompareHypothesis.r
CausalR/R/ComputeFinalDistribution.r
CausalR/R/ComputePValueFromDistributionTable.r
CausalR/R/CreateCCG.r
CausalR/R/CreateCG.r
CausalR/R/CreateNetworkFromTable.r
CausalR/R/DetermineInteractionTypeOfPath.r
CausalR/R/FindApproximateValuesThatWillMaximiseDValue.r
CausalR/R/FindIdsOfConnectedNodesInSubgraph.r
CausalR/R/FindMaximumDValue.r
CausalR/R/GetAllPossibleRoundingCombinations.r
CausalR/R/GetApproximateMaximumDValueFromThreeByTwoContingencyTable.r
CausalR/R/GetApproximateMaximumDValueFromTwoByTwoContingencyTable.r
CausalR/R/GetCombinationsOfCorrectandIncorrectPredictions.r
CausalR/R/GetExplainedNodesOfCCG.r
CausalR/R/GetInteractionInformation.r
CausalR/R/GetMatrixOfCausalRelationships.r
CausalR/R/GetMaxDValueForAFamily.r
CausalR/R/GetMaxDValueForAThreeByTwoFamily.r
CausalR/R/GetMaximumDValueFromTwoByTwoContingencyTable.r
CausalR/R/GetNodeID.r
CausalR/R/GetNodeName.r
CausalR/R/GetNumberOfPositiveAndNegativeEntries.r
CausalR/R/GetPathsInSifFormat.r
CausalR/R/GetRegulatedNodes.r
CausalR/R/GetRowAndColumnSumValues.r
CausalR/R/GetScoreForNumbersOfCorrectandIncorrectPredictions.r
CausalR/R/GetScoresForSingleNode.r
CausalR/R/GetScoresWeightsMatrix.r
CausalR/R/GetScoresWeightsMatrixByCubicAlg.r
CausalR/R/GetSetOfDifferentiallyExpressedGenes.r
CausalR/R/GetSetOfSignificantPredictions.r
CausalR/R/GetShortestPathsFromCCG.r
CausalR/R/GetWeightForNumbersOfCorrectandIncorrectPredictions.r
CausalR/R/GetWeightsAboveHypothesisScoreAndTotalWeights.r
CausalR/R/GetWeightsAboveHypothesisScoreForAThreeByTwoTable.r
CausalR/R/GetWeightsFromInteractionInformation.r
CausalR/R/MakePredictions.r
CausalR/R/MakePredictionsFromCCG.r
CausalR/R/MakePredictionsFromCG.r
CausalR/R/OrderHypotheses.r
CausalR/R/PlotGraphWithNodeNames.r
CausalR/R/PopulateTheThreeByThreeContingencyTable.r
CausalR/R/PopulateTwoByTwoContingencyTable.r
CausalR/R/ProcessExperimentalData.r
CausalR/R/RankTheHypotheses.r
CausalR/R/ReadExperimentalData.r
CausalR/R/ReadSifFileToTable.r
CausalR/R/RemoveIDsNotInExperimentalData.r
CausalR/R/ScoreHypothesis.r
CausalR/R/ValidateFormatOfDataTable.r
CausalR/R/ValidateFormatOfTable.r
CausalR/R/WriteExplainedNodesToSifFile.r
CausalR/R/runRankHypothesis.r
CausalR/R/runSCANR.r
CausalR/build
CausalR/build/vignette.rds
CausalR/inst
CausalR/inst/doc
CausalR/inst/doc/CausalR.R
CausalR/inst/doc/CausalR.Rnw
CausalR/inst/doc/CausalR.pdf
CausalR/inst/extdata
CausalR/inst/extdata/testData.txt
CausalR/inst/extdata/testData1.txt
CausalR/inst/extdata/testNetwork.sif
CausalR/inst/extdata/testNetwork1.sif
CausalR/inst/testData
CausalR/inst/testData/CCGWithTwoLevels.txt
CausalR/inst/testData/network_with_conflict.sif
CausalR/inst/testData/network_with_difflength_conflict.sif
CausalR/inst/testData/network_with_loop.sif
CausalR/inst/testData/test_ExperimentalData.txt
CausalR/inst/testData/test_network.sif
CausalR/inst/unitTests
CausalR/inst/unitTests/CCGWithTwoLevels.txt
CausalR/inst/unitTests/CheckEdgeForTest_SifFileReader.r
CausalR/inst/unitTests/CreateCGForTest_RankTheHypotheses.r
CausalR/inst/unitTests/CreateInteractionInfoTableForTest_SifFileReader.r
CausalR/inst/unitTests/CreateNetworkForTest_SifFileReader.r
CausalR/inst/unitTests/CreateSimpleNetworkForTest_ComputationalCausalGraphCreator.r
CausalR/inst/unitTests/CreateTestTableForTest_SifFileReader.r
CausalR/inst/unitTests/DetermineInteractionTypeOfPath.r
CausalR/inst/unitTests/GetMatrixOfCausalRelationships.r
CausalR/inst/unitTests/RemoveIDsNotInExperimentalData.r
CausalR/inst/unitTests/network_with_conflict.sif
CausalR/inst/unitTests/network_with_difflength_conflict.sif
CausalR/inst/unitTests/network_with_loop.sif
CausalR/inst/unitTests/test_CausalReasoningPredictions.R
CausalR/inst/unitTests/test_CubicAlgorithm.R
CausalR/inst/unitTests/test_CubicAlgorithm1b.R
CausalR/inst/unitTests/test_EnrichmentPValueCalculation.R
CausalR/inst/unitTests/test_ExperimentalData.txt
CausalR/inst/unitTests/test_ExperimentalDataReader.R
CausalR/inst/unitTests/test_HypothesisScorer.R
CausalR/inst/unitTests/test_InputNodes.txt
CausalR/inst/unitTests/test_QuarticAlgorithm.R
CausalR/inst/unitTests/test_RankTheHypotheses.R
CausalR/inst/unitTests/test_SifFileReader.R
CausalR/inst/unitTests/test_SignificanceCalculator.R
CausalR/inst/unitTests/test_WriteExplainedNodesToSifFile.R
CausalR/inst/unitTests/test_network.sif
CausalR/man
CausalR/man/AddIDsToVertices.Rd CausalR/man/AddWeightsToEdges.Rd CausalR/man/AnalyseExperimentalData.Rd CausalR/man/AnalysePredictionsList.Rd CausalR/man/CalculateEnrichmentPValue.Rd CausalR/man/CalculateSignificance.Rd CausalR/man/CalculateSignificanceUsingCubicAlgorithm.Rd CausalR/man/CalculateSignificanceUsingCubicAlgorithm1b.Rd CausalR/man/CalculateSignificanceUsingQuarticAlgorithm.Rd CausalR/man/CalculateTotalWeightForAllContingencyTables.Rd CausalR/man/CalculateWeightGivenValuesInThreeByThreeContingencyTable.Rd CausalR/man/CausalR-package.Rd CausalR/man/CheckPossibleValuesAreValid.Rd CausalR/man/CheckRowAndColumnSumValuesAreValid.Rd CausalR/man/CompareHypothesis.Rd CausalR/man/ComputeFinalDistribution.Rd CausalR/man/ComputePValueFromDistributionTable.Rd CausalR/man/CreateCCG.Rd CausalR/man/CreateCG.Rd CausalR/man/CreateNetworkFromTable.Rd CausalR/man/DetermineInteractionTypeOfPath.Rd CausalR/man/FindApproximateValuesThatWillMaximiseDValue.Rd CausalR/man/FindIdsOfConnectedNodesInSubgraph.Rd CausalR/man/FindMaximumDValue.Rd CausalR/man/GetAllPossibleRoundingCombinations.Rd CausalR/man/GetApproximateMaximumDValueFromThreeByTwoContingencyTable.Rd CausalR/man/GetApproximateMaximumDValueFromTwoByTwoContingencyTable.Rd CausalR/man/GetCombinationsOfCorrectandIncorrectPredictions.Rd CausalR/man/GetExplainedNodesOfCCG.Rd CausalR/man/GetInteractionInformation.Rd CausalR/man/GetMatrixOfCausalRelationships.Rd CausalR/man/GetMaxDValueForAFamily.Rd CausalR/man/GetMaxDValueForAThreeByTwoFamily.Rd CausalR/man/GetMaximumDValueFromTwoByTwoContingencyTable.Rd CausalR/man/GetNodeID.Rd CausalR/man/GetNodeName.Rd CausalR/man/GetNumberOfPositiveAndNegativeEntries.Rd CausalR/man/GetPathsInSifFormat.Rd CausalR/man/GetRegulatedNodes.Rd CausalR/man/GetRowAndColumnSumValues.Rd CausalR/man/GetScoreForNumbersOfCorrectandIncorrectPredictions.Rd CausalR/man/GetScoresForSingleNode.Rd CausalR/man/GetScoresWeightsMatrix.Rd CausalR/man/GetScoresWeightsMatrixByCubicAlg.Rd CausalR/man/GetSetOfDifferentiallyExpressedGenes.Rd CausalR/man/GetSetOfSignificantPredictions.Rd CausalR/man/GetShortestPathsFromCCG.Rd CausalR/man/GetWeightForNumbersOfCorrectandIncorrectPredictions.Rd CausalR/man/GetWeightsAboveHypothesisScoreAndTotalWeights.Rd CausalR/man/GetWeightsAboveHypothesisScoreForAThreeByTwoTable.Rd CausalR/man/GetWeightsFromInteractionInformation.Rd CausalR/man/MakePredictions.Rd CausalR/man/MakePredictionsFromCCG.Rd CausalR/man/MakePredictionsFromCG.Rd CausalR/man/OrderHypotheses.Rd CausalR/man/PlotGraphWithNodeNames.Rd CausalR/man/PopulateTheThreeByThreeContingencyTable.Rd CausalR/man/PopulateTwoByTwoContingencyTable.Rd CausalR/man/ProcessExperimentalData.Rd CausalR/man/RankTheHypotheses.Rd CausalR/man/ReadExperimentalData.Rd CausalR/man/ReadSifFileToTable.Rd CausalR/man/RemoveIDsNotInExperimentalData.Rd CausalR/man/ScoreHypothesis.Rd CausalR/man/ValidateFormatOfDataTable.Rd CausalR/man/ValidateFormatOfTable.Rd CausalR/man/WriteExplainedNodesToSifFile.Rd CausalR/man/runRankHypothesis.Rd CausalR/man/runSCANR.Rd
CausalR/tests
CausalR/tests/runTests.R
CausalR/vignettes
CausalR/vignettes/CausalR-concordance.tex
CausalR/vignettes/CausalR.Rnw
CausalR/vignettes/CausalR.bbl
CausalR/vignettes/CausalR.blg
CausalR/vignettes/DifferentialData.txt
CausalR/vignettes/Fig1.png
CausalR/vignettes/Fig2.png
CausalR/vignettes/Fig3.png
CausalR/vignettes/figure
CausalR/vignettes/figure/unnamed-chunk-4-1.pdf
CausalR/vignettes/figure/unnamed-chunk-6-1.pdf

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