LRDataset: Method "LRDataset"

In PhenStat: Statistical analysis of phenotypic data

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.

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.

Examples

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

PhenStat documentation built on Nov. 8, 2020, 8:13 p.m.