for.exercise {chopsticks} | R Documentation

## Data for exercise in use of the snpMatrix package

### 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)

[Package chopsticks version 1.60.0 Index]