GenABEL (version 1.8-0)

perid.summary: 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

Value

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

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.

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"])