chopsticks (version 1.36.0)

testdata: Test data for the snpMatrix package

Description

This dataset comprises several data frames from a fictional (and unrealistically small) study. The dataset started off as real data from a screen of non-synonymous SNPs for association with type 1 diabetes, but the original identifiers have been removed and a random case/control status has been generated.

Usage

data(testdata)

Format

There are five data objects in the dataset:

• AutosomesAn object of class "snp.matrix" containing genotype calls for 400 subjects at 9445 autosomal SNPs
• XchromosomeAn object of class "X.snp.matrix" containing genotype calls for 400 subjects at 155 SNPs on the X chromosome
• AsnpsA dataframe containing information about the autosomal SNPs. Here it contains only one variable, chromosome, indicating the chromosomes on which the SNPs are located
• XsnpsA dataframe containing information about the X chromosome SNPs. Here it is empty and is only included for completeness
• subject.dataA dataframe containing information about the subjects from whom each row of SNP data was obtained. Here it contains:
  • ccCase-control status
  • sexSex
  • regionGeographical region of residence

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(testdata)
Autosomes
Xchromosome
summary(Asnps)
summary(Xsnps)
summary(subject.data)
summary(summary(Autosomes))
summary(summary(Xchromosome))