vectorOutput: Method "vectorOutput"
In PhenStat: Statistical analysis of phenotypic data

Description Usage Arguments Value Author(s) References See Also Examples

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).

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

`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

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

Natalja Kurbatova, Natasha Karp, Jeremy Mason

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.

PhenTestResult

    # 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)