for.exercise: Data for exercise in use of the snpMatrix package

In chopsticks: The 'snp.matrix' and 'X.snp.matrix' Classes

Description

These data have been created artificially from publicly available datasets. The SNPs have been selected from those genotyped by the International HapMap Project (http://www.hapmap.org) to represent the typical density found on a whole genome association chip, (the Affymetrix 500K platform, http://www.affymetrix.com/support/technical/sample\_data/500k\_hapmap\_genotype\_data.affx for a moderately sized chromosome (chromosome 10). A study of 500 cases and 500 controls has been simulated allowing for recombination using beta software from Su and Marchini (http://www.stats.ox.ac.uk/~marchini/software/gwas/hapgen.html). Re-sampling of cases was weighted in such a way as to simulate three “causal” locus on this chromosome, with multiplicative effects of 1.3, 1.4 and 1.5 for each copy of the risk allele.

Usage

data(for.exercise)

Format

There are three data objects in the dataset:

• snps.10 An object of class "snp.matrix" containing a matrix of SNP genotype calls. Rows of the matrix correspond to subjects and columns correspond to SNPs.

• snp.support A conventional R data frame containing information about the SNPs typed (the chromosome position and the nucleotides corresponding to the two alleles of the SNP).

• subject.support A conventional R dataframe containing information about the study subjects. There are two variables; cc gives case/control status (1=case), and stratum gives ethnicity.

Source

The data were obtained from the diabetes and inflammation laboratory (see http://www-gene.cimr.cam.ac.uk/todd)

References

http://www-gene.cimr.cam.ac.uk/clayton

Examples

data(for.exercise)
snps.10
summary(summary(snps.10))
summary(snp.support)
summary(subject.support)

chopsticks documentation built on Nov. 8, 2020, 7:51 p.m.