for.exercise {snpMatrix} | R Documentation |
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.
data(for.exercise)
There are three data objects in the dataset:
snps.10
snp.matrix
"
containing a matrix of SNP genotype calls. Rows of the matrix
correspond to subjects and columns correspond to SNPs.
snp.support
subject.support
cc
gives case/control
status (1=case), and stratum
gives ethnicity.
The data were obtained from the diabetes and inflammation laboratory (see http://www-gene.cimr.cam.ac.uk/todd)
http://www-gene.cimr.cam.ac.uk/clayton
data(for.exercise) snps.10 summary(summary(snps.10)) summary(snp.support) summary(subject.support)