hom {GenABEL}R Documentation

function to compute average homozygosity within a person

Description

This function computes average homozygosity for a set of people, across multiple markers. Can be used for Quality Control (e.g. contamination checks)

Usage

        hom(data, snpsubset, idsubset, weight="no")

Arguments

data Object of gwaa.data-class or snp.data-class
snpsubset Subset of SNPs to be used
idsubset People for whom average homozygosity is to be computed
weight When "no", homozygosity is computed as a proportion of homozygous genotypes. When "freq", homozygosity is computed as a sum over one minus the frequency of the homozygous allele, and then divided by the number of genotypes.

Details

Value

A matrix with rows corresponding to the ID names and colums showing the number of genotypes measured (NoMeasured) and homozygosity (Hom).

Note

Author(s)

Yurii Aulchenko

References

See Also

ibs, gwaa.data-class, snp.data-class

Examples

data(ge03d2)
h <- hom(ge03d2[,c(1:100)])
homsem <- h[,"Hom"]*(1-h[,"Hom"])/h[,"NoMeasured"]
plot(h[,"Hom"],homsem)

[Package GenABEL version 1.1-8 Index]