genos2mat

A character vector of alleles (e.g. <code>genos[,i,j]</code>) for all genotyped individual.


A matrix for each locus is constructed with n rows and c columns, where n is the number of genotype individuals, and c is the total number of observed alleles at a locus. Individual are surveyed for alleles and assigned 0 for an absence, 0.5 for a single presence (i.e. heterozygote), and 1 for double presence (i.e. homozygote).


internal

Allows the calculation of both genetic diversity partition
statistics, genetic differentiation statistics, and locus informativeness
for ancestry assignment.
It also provides users with various option to calculate
bootstrapped 95\% confidence intervals both across loci,
for pairwise population comparisons, and to plot these results interactively.
Parallel computing capabilities and pairwise results without
bootstrapping are provided.
Weir and Cockerham's 1984 F-statistics are also calculated.
Various plotting features are also provided, as well as Chi-square tests of
genetic heterogeneity are also provided.
Functionality for the calculation of various diversity parameters is
possible for RAD-seq derived SNP data sets containing thousands of marker loci.
A shiny application for the development of microsatellite multiplexes is
also available.

genos2mat: Convert genos loci into presance absence matrices

Description

Usage

Arguments