design score for the model to be tested

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Description

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.

Usage

1
design.score(Mi,model,ploidy,min.MAF,max.geno.freq)

Arguments

Mi

marker to be used

model

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)

ploidy

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

min.MAF

minimum minor allele frequency

max.geno.freq

1 - min.MAF

Value

$S

an incidence matrix for the marker based on the model provided.

See Also

The core function of the package mmer

Examples

1
# it works internally in the \code{\link{mmer}} function

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