design.score

model to be used for designing the matrix. The default is "additive" which can be extend to any ploidy level but alternative models for polyploids such as "additive","1-dom-alt","1-dom-ref","2-dom-alt","2-dom-ref" are supported based on Rosyara (2016)

model

A numeric value indicating the ploidy level of the organism. The default is 2 which means diploid but higher ploidy levels are supported.

ploidy

min.MAF

max.geno.freq

This function is a wrapper from the GWASpoly package that creates the incidence matrix to be used when calculating the -log10 scores for the markers once the variance components and marker effects are estimated.

Mixed model equation solver allowing the specification of variance covariance structures of random effects and residual structures. ML/REML estimates are obtained using the Average Information and/or Expectation-Maximization algorithms. Designed for genomic prediction and genome wide association studies (GWAS) to include additive, dominant and epistatic relationship structures.

design.score: design score for the model to be tested

Description

Usage

Arguments

Value

Examples