mat_pw_dps: Compute a pairwise genetic distance matrix between...

In graph4lg: Build Graphs for Landscape Genetics Analysis

Compute a pairwise genetic distance matrix between populations using Bowcock et al. (1994) formula

Description

The function computes the pairwise DPS, a genetic distance based on the proportion of shared alleles.

Usage

mat_pw_dps(x)

Arguments

x	An object of class genind

Details

The formula used is inspired from MSA software :

D_{PS}=1-\frac{∑_{d}^{D}∑_{k}^{K}\min (f_{a_{kd}i},f_{a_{kd}j})}{D}

such as a_{kd} is the allele k at locus d D is the total number of loci K is the allele number at each locus γ_{a_{kd^{ij}}}=0 if individuals i and j do not share allele a_{kd} γ_{a_{kd^{ij}}}=1 if one of individuals i and j has a copy of a_{kd} γ_{a_{kd^{ij}}}=2 if both individuals have 2 copies of a_{kd} (homozygotes) f_{a_{kd}i} is allele a_{kd} frequency in individual i (0, 0.5 or 1). More information in : Bowcock et al., 1994 and Microsatellite Analyser software (MSA) manual. This function uses functions from adegenet package Note that in the paper of Bowcock et al. (1994), the denominator is 2D. But, in MSA software manual, the denominator is D.

Value

A pairwise matrix of genetic distances between populations

Author(s)

P. Savary

References

\insertRef

bowcock1994highgraph4lg

Examples

data("data_ex_genind")
dist_bowcock <- mat_pw_dps(data_ex_genind)

graph4lg documentation built on Feb. 16, 2023, 5:43 p.m.