htestPhenStat-class {PhenStat} | R Documentation

## Class "htestPhenStat"

### Description

Extension of htest class for the PhenStat needs

### Value

Empty.

### 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")`: ...

### Author(s)

Natalja Kurbatova

### See Also

`htest-class`

### Examples

        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)

[Package PhenStat version 2.26.0 Index]