row.summary {snpMatrix}R Documentation

Summarize rows of a snp matrix

Description

This function calculates call rates and heterozygosity for each row of a an object of class "snp.matrix"

Usage

row.summary(object)

Arguments

object genotype data as a snp.matrix-class or X.snp.matrix-class object

Value

A data frame with rows corresponding to rows of the input object and with columns/elements:

Call.rate Proportion of SNPs called
Heterozygosity Proportion of called SNPs which are heterozygous

Note

The current version does not deal with the X chromosome differently, so that males are counted as homozygous

Author(s)

David Clayton david.clayton@cimr.cam.ac.uk

Examples

data(testdata)
rs <- row.summary(Autosomes)
summary(rs)
rs <- row.summary(Xchromosome)
summary(rs)

[Package snpMatrix version 1.6.1 Index]