PhenTestResult: Method "PhenTestResult"

In PhenStat: Statistical analysis of phenotypic data

Description

Creates PhenTestResult object based on test results or model building results. Internal function for the package. Not build for users to directly call.

Usage

    PhenTestResult(model.output=NULL, model.dataset=NULL,
            depVariable=NULL, 
            refGenotype=NULL,
            equation="withWeight", 
            method="MM", model.effect.batch=NULL, 
            model.effect.variance=NULL,model.effect.sex=NULL, 
            model.effect.interaction=NULL, model.output.interaction=NULL, 
            model.effect.weight=NULL, numberSexes=NULL,pThreshold=0.05, 
            model.formula.null=NULL,model.formula.genotype=NULL, 
            model.output.genotype.nulltest.pVal=NULL, 
            model.output.quality=NULL,model.output.summary=NULL,
            model.output.averageRefGenotype = NULL,
            model.output.percentageChanges = NULL) 

Arguments

model.output	representing the model fit gls object or lme object
model.dataset	dataset used for modeling
depVariable	depending variable in the model
refGenotype	reference genotype in the model
equation	possible values: "withWeight" to include weight effect into model, "withoutWeight" to exclude weight effect from the model
method	possible values: "MM" to work with Mixed Model framework, "FE" to work with Fisher Exact Test framework
model.effect.batch	Result of the test for batch effect significance
model.effect.variance	Result of the test for residual variance effect
model.effect.sex	Result of the test for sex effect significance
model.effect.weight	Result of the test for weight effect significance
model.effect.interaction	Result of the test for genotype by sex interaction significance
model.output.interaction	Interaction test result: p-value
numberSexes	number of possible sex values in the dataset
pThreshold	p-value threshold used to evaluate the effect significance, default value 0.05
model.formula.null	formula for the model without genotype effect
model.formula.genotype	formula for the model with genotype effect
model.output.genotype.nulltest.pVal	Genotype test results: p-value
model.output.quality	vector that contains diagnostic test output for mixed model quality of fit
model.output.summary	named vector that contains summary of the model output
model.output.averageRefGenotype	named vector that contains mean values calculated for reference genotype records
model.output.percentageChanges	named vector that contains percentage changes values per sex

Value

Returns an 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

Examples

    file <- system.file("extdata", "test1.csv", package="PhenStat")
    test <- PhenStat:::PhenList(dataset=read.csv(file,na.strings = '-'),
            testGenotype="Sparc/Sparc")
    # "testDataset" function calls "PhenTestResult" function internally
    result <- PhenStat:::testDataset(test,
            equation="withoutWeight",
            depVariable="Lean.Mass")
    class(result)

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