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hapsim (version 0.31)

divlocus: Diversity score

Description

Compute a measure of genetic diversity at each locus

Usage

divlocus(dat)

Arguments

dat

A binary matrix, rows are haplotypes and columns are binary markers

Value

A vector containing the diversity measure for all markers

Details

This function implements a measure of diversity for a locus \(j\) as in Clayton (2002). If \(z_ij\) represents the allele \(j\) of haplotype \(i\), for \(i=1,...,N\) and assuming that alleles are coded as 0 and 1, the diversity measure can be written as $$D_j = 2*N( \sum_{i=1}^N z_{ij}^2 - (\sum_{i=1}^N z_{ij}) ^2 )$$

References

D. Clayton. Choosing a set of haplotype tagging SNPs from a larger set of diallelic loci. 2002. www-gene.cimr.cam.ac.uk/clayton/software/stata/htSNP/htsnp.pdf

Examples

Run this code
data(ACEdata)
divlocus(ACEdata)

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