matching {hierfstat}

Estimates matching between pairs of individuals

Description

Estimates matching between pairs of individuals (for each locus, gives 1 if the two individuals are homozygous for the same allele, 0 if they are homozygous for a different allele, and 1/2 if at least one individual is heterozygous. Matching is the average of these 0, 1/2 and 1s)

Usage

matching(dos)

Arguments

dos

A matrix of 0, 1 and 2s with loci (SNPs) in columns and individuals in rows. missing values are allowed

Details

This function is written for dosage data, i.e., how many doses of an allele (0, 1 or 2) an individual carries. It should be use for bi-allelic markers only (e.g. SNPs), although you might "force" a k multiallelic locus to k biallelic loci (see fstat2dos).

Value

a matrix of pairwise matching