PhenTestResult {PhenStat} | R Documentation

## 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.

### 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)

[Package PhenStat version 2.28.0 Index]