vectorOutput {PhenStat} | R Documentation

## Method "vectorOutput"

### Description

Wrapper for the model fitting results. Returns model fitting and testing results in a vector format. Assumes that modelling results are stored in the `PhenTestResult` object (output from function `testDataset`).

### Usage

    vectorOutput(
    	phenTestResult,
    	phenotypeThreshold = 0.01,
    	othercolumns = NULL,
    	quote  = '"'
    )

### 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
`othercolumns` | a vector of column names that needs to be included in the function output
`quote` | The charachter that is used to encompass the JSON keys in summary statistics. The default is quotation

### Value

Returns a vector with model fitting results: model output summary and other values

### 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:::vectorOutput(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:::vectorOutput(result2)

[Package PhenStat version 2.18.0 Index]