finalLRModel: Method "finalLRModel"

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/LogisticFramework.R

Description

This is an internal function run within LR framework. It completes the final stage of the LR framework, which builds the final model and estimates effects. As an internal function, it doesn't include extensive error testing of inputs. Please use cautiously if calling directly.

Works with PhenTestResult object created by startLRModel function. The creation of LR final model is based on the significance of different fixed effects, depVariable and equation values stored in PhenTestResult object.

Usage

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    finalLRModel(phenTestResult, 
				outputMessages = TRUE)

Arguments

phenTestResult

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

outputMessages

flag: "FALSE" value to suppress output messages; "TRUE" value to show output messages; default value TRUE

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

PhenTestResult and testDataset

Examples

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    file <- system.file("extdata", "testLR.csv", package="PhenStat")
    testLR <- PhenStat:::PhenList(dataset=read.csv(file,na.strings = '-'),
            testGenotype="Mock")
    testLR2 <- PhenStat:::LRDataset(testLR,"V2")
    
    # when "testDataset" function's argument "callAll" is set to FALSE 
    # only "startLRModel" function is called - the first step of LR framework
    resultLR <- PhenStat:::testDataset(testLR2,
            depVariable="V2",
            callAll=FALSE,
            method="LR")
    # print out formula that has been created
    PhenStat:::analysisResults(resultLR)$model.formula.genotype
    # print out batch effect's significance 
    PhenStat:::analysisResults(resultLR)$model.effect.batch
    resultLR <- PhenStat:::finalLRModel(resultLR)

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