vectorOutput {PhenStat} | R Documentation |
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 |
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.
# 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)