PhenStat (version 2.6.0)

LRDataset: Method "LRDataset"

Description

Prepares dataset for the LR framework - maps values of dependent variable to 0/1, where 1 is modeled.

Usage

LRDataset(phenList = NULL, depVariable = NULL, abnormalValues = c("abnormal", "Abnormal", "TRUE", "deviant"), outputMessages = TRUE)

Arguments

phenList

instance of the PhenList class; mandatory argument

depVariable

a character string defining the dependent variable of interest; mandatory argument

abnormalValues

a list of abnormal values that will be mapped to 0; mandatory argument

outputMessages

flag: "FALSE" value to suppress output messages; "TRUE" value to show output messages; default value TRUE

Value

Returns dataset suitable for LR framework, where provided abonormal values are mapped to 1 and all other values of dependent variable are assumed to be normal and are mapped to 0.

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.

Examples

    file <- system.file("extdata", "testLR.csv", package="PhenStat")
    testLR <- PhenList(dataset=read.csv(file),
            testGenotype="Mock")
    testLR2 <- LRDataset(testLR,"V2")