snpStats: testdata – R documentation

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testdata

Test data for the snpStats 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:

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))

snpStats

SnpMatrix and XSnpMatrix classes and methods

v1.40.0

GPL-3

Authors

David Clayton <dc208@cam.ac.uk>

Initial release

2019-10-08