htestPhenStat-class: Class "htestPhenStat"

Description

Extension of htest class for the PhenStat needs

Arguments

Explore htestPhenStat object

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

Slots

modelOutput:: Object of class "htest" ~~
analysedSubset:: Object of class "character" ~~
comparison:: Object of class "character" ~~
ES:: Object of class "numeric" ~~
matrixCount:: Object of class "matrix" ~~

Methods

getColumnView: signature(obj = "htestPhenStat"): ...
getMatrix: signature(obj = "htestPhenStat"): ...
getPercentageMatrix: signature(obj = "htestPhenStat"): ...
subsetText: signature(object = "htestPhenStat"): ...
comparison: signature(object = "htestPhenStat"): ...
show: signature(object = "htestPhenStat"): ...

Examples

Run this code

    file <- system.file("extdata", "test_categorical.csv", package="PhenStat")
    test <- PhenList(dataset=read.csv(file),
            testGenotype="Aff3/Aff3")
    # "FisherExactTest" function is called from "testDataset" function.
    result <- testDataset(test,depVariable="Thoracic.Processes",method="FE")  
    # Fisher Exact Test results can be printed out using function "summaryOutput"
    val <- analysisResults(result)[[1]]
    print(val)
    class(val)