htestPhenStat-class {PhenStat} | R Documentation |
Extension of htest class for the PhenStat needs
Empty.
A list with "htest" components in modelOutput slot and the additional PhenStat specific slots:
1. modelOutput: htest object with Fisher Exact test (fisher.test) output
2. analysedSubset: the subset analysed with possible values "all", "males", "females"
3. comparison: for the RR method with possible values "High vs Normal/Low", "Low vs Normal/High"
4. ES: effect size value
5. matrixCount: matrix of counts used for the test
modelOutput
:Object of class "htest"
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analysedSubset
:Object of class "character"
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comparison
:Object of class "character"
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ES
:Object of class "numeric"
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matrixCount
:Object of class "matrix"
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signature(obj = "htestPhenStat")
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signature(obj = "htestPhenStat")
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signature(obj = "htestPhenStat")
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signature(object = "htestPhenStat")
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signature(object = "htestPhenStat")
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signature(object = "htestPhenStat")
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Natalja Kurbatova
file <- system.file("extdata", "test_categorical.csv", package="PhenStat") test <- PhenStat:::PhenList(dataset=read.csv(file,na.strings = '-'), testGenotype="Aff3/Aff3") # "FisherExactTest" function is called from "testDataset" function. result <- PhenStat:::testDataset(test,depVariable="Thoracic.Processes",method="FE") # Fisher Exact Test results can be printed out using function "summaryOutput" val <- PhenStat:::analysisResults(result)[[1]] print(val) class(val)