PhenTestResult: Method "PhenTestResult"

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.

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")
    # "testDataset" function calls "PhenTestResult" function internally
    result <- testDataset(test,
            equation="withoutWeight",
            depVariable="Lean.Mass")
    class(result)