summaryOutput: Method "summaryOutput"

In PhenStat: Statistical analysis of phenotypic data

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

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

PhenTestResult

Examples

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

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