hapmapchr22 {GeneticsBase} | R Documentation

## Chromosome 22 genotypes from International HapMap project

### Description

The sample data file, hapmapchr22, contains genotypes of hromosome 22 from the International HapMap project. This file contains genotypes from 30 CEPH trios (90 subjects) for all Phase 1 HapMap (about 1 SNP per 3kb on average) - see http://hapmap.org for the original data file, full details of samples, markers and methods. Note that the HapMap data files are deidentified and freely distributable without restriction.

### Usage

    data(hapmapchr22)

### Format

The format is: chr "hapmapchr22"

### Details

The file was created by converting chromosome 22 bulk data download data files from the HapMap file repository at http://hapmap.org/genotypes/2005-06_16c_phaseI/full/non-redundant/

Downloaded HapMap files were converted by transposing the layout of the data from one row per marker to the pedigree file convention of two columns per marker. There are many variants of the pedigree format but these files are compatible with the popular family based analysis software packages FBAT (http://www.biostat.harvard.edu/~fbat/fbat.htm) and PBAT (http://www.biostat.harvard.edu/~clange/default.htm)

The file has a header row containing only the marker names followed by one row per subject. Data rows always start with 6 fields - `family_id`, `individual_id`, `father_id`, `mother_id`, gender and affection status. Parents have zero for `mother_id` and `father_id`. The remaining columns in each row contain two allele codes for each marker. Alleles are coded as $0$ for missing, $1=A$, $2=C$, $3=G$ and $4=T$. All fields in a row are delimited by one or more spaces. Note that affection status was arbitrarily set to 2 (affected) for children and 1 (unaffected) for adults - although in reality, HapMap CEPH subjects were not ascertained for any disease.

### Source

http://hapmap.org/genotypes/2005-06_16c_phaseI/full/non-redundant/

### References

http://www.biostat.harvard.edu/~fbat/fbat.htm http://www.biostat.harvard.edu/~clange/default.htm

### Examples

    data(hapmapchr22)

[Package GeneticsBase version 1.0.0 Index]