gl.pcoa

Name of the genlight object containing the SNP genotypes by specimen and population [required]

Number of dimensions to retain in the output file [default 5]

nfactors

TRUE if parallel processing is required (does fail under Windows) [default FALSE]

parallel

Number of cores to use if parallel processing is requested [default 16]

n.cores

-- verbose if TRUE, silent if FALSE [default TRUE]

This script takes the data on SNP genotypes for individuals and undertakes a Gower PCoa ordination using Euclidean distance and drawing upon
data in the original genlight {adegenet} object (entity x attribute matrix).
The script is essentially a wrapper for glPca() {adegenet} with default settings apart from setting parallel=FALSE and
converting the eigenvalues to percentages.

Functions are provided that facilitate the import and analysis of
SNP (single nucleotide polymorphism) and silicodart (presence/absence) data. The main focus is on data generated
by DarT (Diversity Arrays Technology). However, once SNP or related fragment
presence/absence data from any source is imported into a genlight object many
of the functions can be used. Functions are available for input and output of
SNP and silicodart data, for reporting on and filtering on various criteria
(e.g. CallRate, Heterozygosity, Reproducibility, maximum allele frequency).
Advanced filtering is based on Linkage Disequilibrium and HWE (Hardy-Weinberg equilibrium). Other functions
are available for visualization after PCoA (Principle Coordinate Analysis), or to facilitate transfer of data
between genlight/genind objects and newhybrids, related, phylip, structure, faststructure packages.

gl.pcoa: PCoA ordination (glPca)

Description

Usage

Arguments

Value

Examples