row.summary: Summarize rows of a snp matrix

In chopsticks: The 'snp.matrix' and 'X.snp.matrix' Classes

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 [e-mail]

Examples

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

chopsticks documentation built on Nov. 8, 2020, 7:51 p.m.