mdr1: Sample data for MDR package for n=250, p=25
Description
This dataset provides case/control disease status and genetic information.
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 66.16The 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 |
Genotype |
BB |
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.