RRTest: 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

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.

Examples

Run this code

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