summaryOutput {PhenStat} | R Documentation

## Method "summaryOutput"

### 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)

[Package PhenStat version 2.18.0 Index]