gl.grm

-- a switch if a heatmap should be shown [Default:TRUE]

plotheatmap

switch if loci with imputed data should be returned (see ?A.mat in package rrBLUP)

return.imputed

-- verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log ; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity]

verbose

parameters passed to function A.mat from package rrBLUP

The G matrix is calculated by centering the allele frequency matrix of the second allele by substracting 2 times the allefrequency

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.grm: Calculates the genomic relatedness matrix

Description

Usage

Arguments

Value

Examples