RRTest {PhenStat} | R Documentation

## Method "RRTest"

### Description

This is an internal function run within RR framework. It performs Reference Ranges Plus test and after that Fisher Exact test on calculated count matrices. As an internal function, it doesn't include extensive error testing of inputs. Please use cautiously if calling directly.

Works with `PhenList` object created by `PhenList` function.

### Usage

        RRTest(
    		  phenList,
    		  depVariable,
    		  outputMessages = TRUE,
    		  naturalVariation = 95,
    		  controlPointsThreshold = 60
    )

### Arguments

`phenList` | instance of the `PhenList` class; mandatory argument
`depVariable` | a character string defining the dependent variable of interest; mandatory argument
`outputMessages` | flag: "FALSE" value to suppress output messages; "TRUE" value to show output messages; default value TRUE
`naturalVariation` | number defining the natural variation range in percents for normal values; default value 95
`controlPointsThreshold` | number defining how many control points is needed to perform RR plus method; default value 60

### Value

Returns results stored in instance of the `PhenTestResult` class

### Author(s)

Natalja Kurbatova, Natasha Karp, Jeremy Mason

### References

Karp N, Melvin D, Sanger Mouse Genetics Project, Mott R (2012): Robust and Sensitive Analysis of Mouse Knockout Phenotypes. PLoS ONE 7(12): e52410. doi:10.1371/journal.pone.0052410

West B, Welch K, Galecki A (2007): Linear Mixed Models: A practical guide using statistical software New York: Chapman & Hall/CRC 353 p.

### See Also

`PhenList` and `testDataset`

### Examples

        file <- system.file("extdata", "test1.csv", package="PhenStat")
        test <- PhenStat:::PhenList(dataset=read.csv(file,na.strings = '-'),
                testGenotype="Sparc/Sparc")
        # "RRTest" function is called from "testDataset" function
        result <- PhenStat:::testDataset(test,
                depVariable="Lean.Mass",
                method="RR")
        # RR test results can be printed out using function "summaryOutput"
        summary(result)

[Package PhenStat version 2.17.0 Index]