CausalR: Causal network analysis methods
Version 1.8.0

Causal network analysis methods for regulator prediction and network reconstruction from genome scale data.

Browse man pages Browse package API and functions Browse package files

AuthorGlyn Bradley, Steven Barrett, Chirag Mistry, Mark Pipe, David Wille, David Riley, Bhushan Bonde, Peter Woollard
Bioconductor views DifferentialExpression GraphAndNetwork Microarray Network Network Inference Proteomics RNASeq SystemsBiology Transcriptomics
Date of publicationNone
MaintainerGlyn Bradley <glyn.x.bradley@gsk.com>, Steven Barrett <steven.j.barrett@gsk.com>
LicenseGPL (>= 2)
Version1.8.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CausalR")

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
WriteAllExplainedNodesToSifFile: Write all explained nodes to Sif file
WriteExplainedNodesToSifFile: Write explained nodes to Sif file

Functions

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

Files

DESCRIPTION
NAMESPACE
R
R/AddIDsToVertices.r
R/AddWeightsToEdges.r
R/AnalyseExperimentalData.r
R/AnalysePredictionsList.r
R/CalculateEnrichmentPValue.r
R/CalculateSignificance.r
R/CalculateSignificanceUsingCubicAlgorithm.r
R/CalculateSignificanceUsingCubicAlgorithm1b.r
R/CalculateSignificanceUsingQuarticAlgorithm.r
R/CalculateTotalWeightForAllContingencyTables.r
R/CalculateWeightGivenValuesInThreeByThreeContingencyTable.r
R/CausalR-package.r
R/CheckPossibleValuesAreValid.r
R/CheckRowAndColumnSumValuesAreValid.r
R/CompareHypothesis.r
R/ComputeFinalDistribution.r
R/ComputePValueFromDistributionTable.r
R/CreateCCG.r
R/CreateCG.r
R/CreateNetworkFromTable.r
R/DetermineInteractionTypeOfPath.r
R/FindApproximateValuesThatWillMaximiseDValue.r
R/FindIdsOfConnectedNodesInSubgraph.r
R/FindMaximumDValue.r
R/GetAllPossibleRoundingCombinations.r
R/GetApproximateMaximumDValueFromThreeByTwoContingencyTable.r
R/GetApproximateMaximumDValueFromTwoByTwoContingencyTable.r
R/GetCombinationsOfCorrectandIncorrectPredictions.r
R/GetExplainedNodesOfCCG.r
R/GetInteractionInformation.r
R/GetMatrixOfCausalRelationships.r
R/GetMaxDValueForAFamily.r
R/GetMaxDValueForAThreeByTwoFamily.r
R/GetMaximumDValueFromTwoByTwoContingencyTable.r
R/GetNodeID.r
R/GetNodeName.r
R/GetNumberOfPositiveAndNegativeEntries.r
R/GetPathsInSifFormat.r
R/GetRegulatedNodes.r
R/GetRowAndColumnSumValues.r
R/GetScoreForNumbersOfCorrectandIncorrectPredictions.r
R/GetScoresForSingleNode.r
R/GetScoresWeightsMatrix.r
R/GetScoresWeightsMatrixByCubicAlg.r
R/GetSetOfDifferentiallyExpressedGenes.r
R/GetSetOfSignificantPredictions.r
R/GetShortestPathsFromCCG.r
R/GetWeightForNumbersOfCorrectandIncorrectPredictions.r
R/GetWeightsAboveHypothesisScoreAndTotalWeights.r
R/GetWeightsAboveHypothesisScoreForAThreeByTwoTable.r
R/GetWeightsFromInteractionInformation.r
R/MakePredictions.r
R/MakePredictionsFromCCG.r
R/MakePredictionsFromCG.r
R/OrderHypotheses.r
R/PlotGraphWithNodeNames.r
R/PopulateTheThreeByThreeContingencyTable.r
R/PopulateTwoByTwoContingencyTable.r
R/ProcessExperimentalData.r
R/RankTheHypotheses.r
R/ReadExperimentalData.r
R/ReadSifFileToTable.r
R/RemoveIDsNotInExperimentalData.r
R/ScoreHypothesis.r
R/ValidateFormatOfDataTable.r
R/ValidateFormatOfTable.r
R/WriteAllExplainedNodesToSifFile.r
R/WriteExplainedNodesToSifFile.r
R/runRankHypothesis.r
R/runSCANR.r
build
build/vignette.rds
inst
inst/doc
inst/doc/CausalR.R
inst/doc/CausalR.pdf
inst/doc/CausalR.rnw
inst/extdata
inst/extdata/testData.txt
inst/extdata/testData1.txt
inst/extdata/testNetwork.sif
inst/extdata/testNetwork1.sif
inst/testData
inst/testData/CCGWithTwoLevels.txt
inst/testData/network_with_conflict.sif
inst/testData/network_with_difflength_conflict.sif
inst/testData/network_with_loop.sif
inst/testData/test_ExperimentalData.txt
inst/testData/test_network.sif
inst/unitTests
inst/unitTests/CCGWithTwoLevels.txt
inst/unitTests/CheckEdgeForTest_SifFileReader.r
inst/unitTests/CreateCGForTest_RankTheHypotheses.r
inst/unitTests/CreateInteractionInfoTableForTest_SifFileReader.r
inst/unitTests/CreateNetworkForTest_SifFileReader.r
inst/unitTests/CreateSimpleNetworkForTest_ComputationalCausalGraphCreator.r
inst/unitTests/CreateTestTableForTest_SifFileReader.r
inst/unitTests/DetermineInteractionTypeOfPath.r
inst/unitTests/GetMatrixOfCausalRelationships.r
inst/unitTests/RemoveIDsNotInExperimentalData.r
inst/unitTests/network_with_conflict.sif
inst/unitTests/network_with_difflength_conflict.sif
inst/unitTests/network_with_loop.sif
inst/unitTests/test_CausalReasoningPredictions.R
inst/unitTests/test_CubicAlgorithm.R
inst/unitTests/test_CubicAlgorithm1b.R
inst/unitTests/test_EnrichmentPValueCalculation.R
inst/unitTests/test_ExperimentalData.txt
inst/unitTests/test_ExperimentalDataReader.R
inst/unitTests/test_HypothesisScorer.R
inst/unitTests/test_InputNodes.txt
inst/unitTests/test_NodeInclusionFile.txt
inst/unitTests/test_QuarticAlgorithm.R
inst/unitTests/test_RankTheHypotheses.R
inst/unitTests/test_SifFileReader.R
inst/unitTests/test_SignificanceCalculator.R
inst/unitTests/test_WriteExplainedNodesToSifFile.R
inst/unitTests/test_network.sif
man
man/AddIDsToVertices.Rd
man/AddWeightsToEdges.Rd
man/AnalyseExperimentalData.Rd
man/AnalysePredictionsList.Rd
man/CalculateEnrichmentPValue.Rd
man/CalculateSignificance.Rd
man/CalculateSignificanceUsingCubicAlgorithm.Rd
man/CalculateSignificanceUsingCubicAlgorithm1b.Rd
man/CalculateSignificanceUsingQuarticAlgorithm.Rd
man/CalculateTotalWeightForAllContingencyTables.Rd
man/CalculateWeightGivenValuesInThreeByThreeContingencyTable.Rd
man/CausalR-package.Rd
man/CheckPossibleValuesAreValid.Rd
man/CheckRowAndColumnSumValuesAreValid.Rd
man/CompareHypothesis.Rd
man/ComputeFinalDistribution.Rd
man/ComputePValueFromDistributionTable.Rd
man/CreateCCG.Rd
man/CreateCG.Rd
man/CreateNetworkFromTable.Rd
man/DetermineInteractionTypeOfPath.Rd
man/FindApproximateValuesThatWillMaximiseDValue.Rd
man/FindIdsOfConnectedNodesInSubgraph.Rd
man/FindMaximumDValue.Rd
man/GetAllPossibleRoundingCombinations.Rd
man/GetApproximateMaximumDValueFromThreeByTwoContingencyTable.Rd
man/GetApproximateMaximumDValueFromTwoByTwoContingencyTable.Rd
man/GetCombinationsOfCorrectandIncorrectPredictions.Rd
man/GetExplainedNodesOfCCG.Rd
man/GetInteractionInformation.Rd
man/GetMatrixOfCausalRelationships.Rd
man/GetMaxDValueForAFamily.Rd
man/GetMaxDValueForAThreeByTwoFamily.Rd
man/GetMaximumDValueFromTwoByTwoContingencyTable.Rd
man/GetNodeID.Rd
man/GetNodeName.Rd
man/GetNumberOfPositiveAndNegativeEntries.Rd
man/GetPathsInSifFormat.Rd
man/GetRegulatedNodes.Rd
man/GetRowAndColumnSumValues.Rd
man/GetScoreForNumbersOfCorrectandIncorrectPredictions.Rd
man/GetScoresForSingleNode.Rd
man/GetScoresWeightsMatrix.Rd
man/GetScoresWeightsMatrixByCubicAlg.Rd
man/GetSetOfDifferentiallyExpressedGenes.Rd
man/GetSetOfSignificantPredictions.Rd
man/GetShortestPathsFromCCG.Rd
man/GetWeightForNumbersOfCorrectandIncorrectPredictions.Rd
man/GetWeightsAboveHypothesisScoreAndTotalWeights.Rd
man/GetWeightsAboveHypothesisScoreForAThreeByTwoTable.Rd
man/GetWeightsFromInteractionInformation.Rd
man/MakePredictions.Rd
man/MakePredictionsFromCCG.Rd
man/MakePredictionsFromCG.Rd
man/OrderHypotheses.Rd
man/PlotGraphWithNodeNames.Rd
man/PopulateTheThreeByThreeContingencyTable.Rd
man/PopulateTwoByTwoContingencyTable.Rd
man/ProcessExperimentalData.Rd
man/RankTheHypotheses.Rd
man/ReadExperimentalData.Rd
man/ReadSifFileToTable.Rd
man/RemoveIDsNotInExperimentalData.Rd
man/ScoreHypothesis.Rd
man/ValidateFormatOfDataTable.Rd
man/ValidateFormatOfTable.Rd
man/WriteAllExplainedNodesToSifFile.Rd
man/WriteExplainedNodesToSifFile.Rd
man/runRankHypothesis.Rd
man/runSCANR.Rd
tests
tests/runTests.R
vignettes
vignettes/CausalR.rnw
vignettes/DifferentialData.txt
vignettes/Fig1.png
vignettes/Fig2.png
vignettes/Fig3.png
vignettes/Fig4.png
vignettes/figure
vignettes/figure/unnamed-chunk-4-1.pdf
vignettes/figure/unnamed-chunk-6-1.pdf
CausalR documentation built on May 20, 2017, 9:42 p.m.