htestPhenStat-class: Class "htestPhenStat"

In PhenStat: Statistical analysis of phenotypic data

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)

PhenStat documentation built on Nov. 8, 2020, 8:13 p.m.