simGWAS: Simulated GWAS data set

In crbasel/hierinf: Hierarchical Inference

Description

The data set simGWAS was simulated using PLINK where the SNPs were binned into different allele frequency ranges. There are 250 controls and 250 cases, i.e. a binary response and 500 subjects. The variables age and sex are two additional control variables. The variables SNP.1 till SNP.990 were simulated to have no association with the response and the variables SNP.991 till SNP.1000 have a population odds ratio of 2.

Usage

data(simGWAS)

Format

A list with three elements:

x

a matrix with 500 rows and 1000 columns where the rows and columns correspond to the subjects and variables, respectively. The variables are named SNP.1, ..., SNP.1000.

y

binary response vector with 500 elements where the elements correspond to the subjects.

clvar

a matrix with 500 rows and 2 columns where the rows and columns correspond to the subjects and variables, respectively. The age of the subject is stored in the variable age. The variable sex takes the value 0 for men and 1 for women.

Source

Buzdugan L (2018). hierGWAS: Asessing statistical significance in predictive GWA studies. R package version 1.10.0.

Examples

data(simGWAS)
sim.geno <- simGWAS$x
sim.pheno <- simGWAS$y
sim.clvar <- simGWAS$clvar

dendr <- cluster_var(x = sim.geno)
set.seed(1234)
result <- test_hierarchy(x = sim.geno, y = sim.pheno,
                         dendr = dendr, clvar = sim.clvar,
                         family = "binomial")

crbasel/hierinf documentation built on April 4, 2020, 1:35 p.m.