testdata: Test data for the snpStats package

In NikNakk/snpStats: SnpMatrix and XSnpMatrix classes and methods

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:

• Autosomes: An object of class "SnpMatrix" containing genotype calls for 400 subjects at 9445 autosomal SNPs

• Xchromosome: An object of class "XSnpMatrix" containing genotype calls for 400 subjects at 155 SNPs on the X chromosome

• Asnps: A dataframe containing information about the autosomal SNPs. Here it contains only one variable, chromosome, indicating the chromosomes on which the SNPs are located

• Xsnps: A dataframe containing information about the X chromosome SNPs. Here it is empty and is only included for completeness

• subject.data: A dataframe containing information about the subjects from whom each row of SNP data was obtained. Here it contains:

  • cc: Case-control status

  • sex: Sex

  • region: Geographical region of residence

Source

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

Examples

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

NikNakk/snpStats documentation built on May 7, 2019, 6:18 p.m.