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

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

Removes of all non-concurrent batches from the dataset. Returns dataset suitable for TF framework or original dataset if data removal was not successful.

    TFDataset(phenList,
          depVariable,
          outputMessages  = TRUE,
          forDecisionTree = FALSE,
          upper           = 5)

`phenList`	instance of the `PhenList` class; mandatory argument
`depVariable`	a character string defining the dependent variable of interest; mandatory argument
`outputMessages`	flag: "FALSE" value to suppress output messages; "TRUE" value to show output messages; default value TRUE
`forDecisionTree`	flag: "FALSE" value for normal procedure; "TRUE" value to indicate that is called form decisionTree function; default value FALSE
`upper`	Single integer: maximum allowed number of levels for the Batch in the TF framework. Default 5.

Returns dataset suitable for TF framework or original dataset if data removal was not successful.

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.

PhenList

    file <- system.file("extdata", "test1.csv", package="PhenStat")
    test <- PhenStat:::PhenList(dataset=read.csv(file,na.strings = '-'),
            testGenotype="Sparc/Sparc")
    test2 <- PhenStat:::TFDataset(test,"Lean.Mass")