Nhlsim {CrypticIBDcheck}R Documentation

Example data for the CrypticIBDcheck package

Description

A dataset that contains genotypes simulated by gene drop based on a model of linkage disequilibrium fit to data from a candidate-gene case-control study. Several close relative pairs have been included in the simulated data.

Usage

data(Nhlsim)

Format

A list comprised of the following four objects:

[[1]] snp.data a snp.matrix object containing genotypes of 208 subjects (108 controls and 100 cases).
Rows correspond to subjects and columns correspond to SNPs
[[2]] chromosome a numeric vector containing the chromosome numbers of the SNPs
[[3]] physmap a numeric vector of physical positions
[[4]] csct a vector of case-control status (1=case, 0=control)

Details

The dataset contains mostly unrelated individuals, but includes two parent-offspring pairs and three full-siblings pairs to show how the CrypticIBDcheck package can be used to uncover cryptic relatedness.

Source

The genotypes were simulated based on data from a candidate-gene case-control study described in Schuetz et al. (2012).

References

Schuetz JM, Daley D, Graham J, Berry BR, Gallagher RP, Connors JM, Gascoyne RD, Spinelli JJ, Brooks-Wilson AR (2012). Genetic Variation in Cell Death Genes and Risk of Non-Hodgkin Lymphoma. PLoS ONE, 7(2), e31560. doi:10.1371/journal.pone.0031560.

Examples

data(Nhlsim)

[Package CrypticIBDcheck version 0.3-3 Index]