# Causal Reasoning Methods

## Documentation for package ‘CausalR’ version 1.6.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

CausalR-package | The CausalR package
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 table
CausalR | 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 superfamily
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 predictions
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 p-value calculation
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