mdr1: Sample data for MDR package for n=250, p=25

In MDR: Detect gene-gene interactions using multifactor dimensionality reduction

Description

This dataset provides case/control disease status and genetic information.

Usage

data(mdr1)

Format

A simulated data frame with 250 observations on 26 variables. 'Response' is a binary vector representing case(1) or control(0) status for a disease. Variables 'SNP.1' to 'SNP.25' are numeric variables which represent genotype information (coded as 0,1,2) at 25 loci.

Details

This data was simulated with an equal number of cases and controls according to a variation on the dominant-dominant model of Neuman and Rice and represents a two-way interaction with main effects at 5 percent heritability. The true disease-causing loci are SNP.4 and SNP.9, generated with minor allele frequency 0.5. The expected balanced accuracy for this model is 66.16

The penetrance function used to generate the case/control data based on the 9 possible genotype combinations is as follows:

Genotype	BB	Bb	bb
AA	0.05	0.05	0.05
Aa	0.05	0.206	0.206
aa	0.05	0.206	0.206

References

Neuman RJ, Rice JP. (1992). TWO-LOCUS MODELS OF DISEASE. Genetic Epidemiology 9(5):347-365.

Culverhouse R, et al (2002). A perspective on epistasis: limits of models displaying no main effect. Am J Hum Genet, 70(2):461-471.

Examples

data(mdr1)

Example output

Loading required package: lattice

MDR documentation built on May 29, 2017, 7:05 p.m.