testdata {chopsticks} | R Documentation

## 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:

- `Autosomes`An object of class `"snp.matrix"` containing genotype calls for 400 subjects at 9445 autosomal SNPs

- `Xchromosome`An object of class `"X.snp.matrix"` 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/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))

[Package chopsticks version 1.54.0 Index]