divlocus {hapsim} | R Documentation |
Compute a measure of genetic diversity at each locus
divlocus(dat)
dat |
A binary matrix, rows are haplotypes and columns are binary markers |
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 )
A vector containing the diversity measure for all markers
Giovanni Montana
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
data(ACEdata) divlocus(ACEdata)