CausalR: Causal Reasoning Methods

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

Author
Glyn Bradley, Steven Barrett, David Wiley, Bhushan Bonde, Peter Woollard, Chirag Mistry, David Riley, Mark Pipe
Date of publication
None
Maintainer
Glyn Bradley <glyn.x.bradley@gsk.com>, Steven Barrett <steven.j.barrett@gsk.com>, Bhushan Bonde <bkbonde@gmail.com>
License
GPL (>= 2)
Version
1.6.0

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

Files in this package

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