Nhlsim: Example data for the CrypticIBDcheck package

In CrypticIBDcheck: Identifying Cryptic Relatedness in Genetic Association Studies

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)

Example output

Loading required package: rJPSGCS
Loading required package: rJava
Loading required package: chopsticks
Loading required package: survival
OpenJDK 64-Bit Server VM warning: Can't detect initial thread stack location - find_vma failed
Loading required package: car
Loading required package: ellipse

Attaching package: 'ellipse'

The following object is masked from 'package:car':

    ellipse

Warning message:
In methods:::bind_activation(TRUE) :
  methods:::bind_activation(TRUE) is deprecated;
 you should rather provide methods for cbind2() / rbind2()
Warning message:
system call failed: Cannot allocate memory 

CrypticIBDcheck documentation built on May 2, 2019, 7:30 a.m.