mdr2: Sample data for MDR package for n=250, p=100

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

Description

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

Usage

data(mdr2)

Format

A simulated data frame with 250 observations on 101 variables. 'Response' is a binary vector representing case(1) or control(0) status for a disease. Variables 'SNP.1' to 'SNP.100' are numeric variables which represent genotype information (coded as 0,1,2) at 100 loci.

Details

This data was simulated with an equal number of cases and controls according to a variation on the purely-epistatic XOR model of Li and Reich and represents a two-way interaction in the absence of marginal 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 67.09

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

Genotype	BB	Bb	bb
AA	0.199	0.05	0.199
Aa	0.05	0.199	0.05
aa	0.199	0.05	0.199

References

Li W, Reich J. 2000. A complete enumeration and classification of two-locus disease models. Hum Hered 50(6):334-49.

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(mdr2)

Example output

Loading required package: lattice

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