summaryOutput: Method "summaryOutput"

Description

Wrapper for the model fitting results. Returns model fitting and testing results in a user friendly format.

Usage

summaryOutput(phenTestResult, phenotypeThreshold = 0.01)

Arguments

phenTestResult

instance of the PhenTestResult class that comes from the function testDataset; mandatory argument

phenotypeThreshold

a numerical value defining the threshold to use in classificationTag; default value 0.01

Value

Returns model fitting results in a text format for the screen

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

    # Mixed Model framework
    file <- system.file("extdata", "test1.csv", package="PhenStat")
    test <- PhenList(dataset=read.csv(file),
            testGenotype="Sparc/Sparc")
    result <- testDataset(test,
            depVariable="Lean.Mass")
    summaryOutput(result)
    
    # Fishe Exact Test framework
    file <- system.file("extdata", "test_categorical.csv", package="PhenStat")
    test2 <- PhenList(dataset=read.csv(file),
            testGenotype="Aff3/Aff3")
    result2 <- testDataset(test2,
            depVariable="Thoracic.Processes",
            method="FE")  
    summaryOutput(result2)