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

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 1.6-7 Index]