testdata {snpStats} | R Documentation

## 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))

[Package snpStats version 1.34.0 Index]