R: Summary of marker data per person

perid.summary {GenABEL} | R Documentation

## Summary of marker data per person

### Description

Produces call rate and heterozygosity per person

### Usage

    perid.summary(data, snpsubset, idsubset, ... )

### Arguments

`data` | object of `snp.data-class`
`snpsubset` | Index, character or logical vector with subset of SNPs to run analysis on. If missing, all SNPs from `data` are used for analysis.
`idsubset` | Index, character or logical vector with subset of IDs to run analysis on. If missing, all people from `data` are used for analysis.
`...` | additional parameters to be passed to `hom`

### Details

This function facilitates quality control of genomic data. E.g. extreme outliers for heterozygosity indicate possibly contaminated DNA samples, while low call rate of a person may indicate poor DNA quality.

### Value

A matrix, giving per person (row) its' average heterozygosity ("Het" column) and call rate ("CallPP"), over all SNPs

### Author(s)

Yurii Aulchenko

### See Also

`check.marker`, `summary.snp.data`, `snp.data-class`

### Examples

    require(GenABEL.data)
    data(ge03d2c)
    a <- perid.summary(data=ge03d2c,snps=c(1:100),ids=c(1:10))
    a
    a <- perid.summary(data=ge03d2c)
    hist(a[,"CallPP"])
    hist(a[,"Het"])

[Package GenABEL version 1.8-0 Index]