NAM (version 1.5.3)

Reference: Changing the Reference Genotype

Description

Function changes the reference genotype. For NAM populations, this function must be used when genotypes are coded according to the reference genome instead of the standard parent.

Usage

reference(gen, ref = NULL)

Arguments

gen

Numeric matrix containing the genotypic data. A matrix with \(n\) rows of observations and (\(m\)) columns of molecular markers. SNPs must be coded as 0, 1, 2.

ref

Numeric vector of length \(n\) with elements coded as 0, 1, 2, it represents the genotypic information of a new reference genotype. Default assumes that more frequent allele represents the reference genome.

Value

Returns a recoded \(gen\) matrix

Details

If genotypes are coded based on the refence genome, NAM analysis are optimized by using the standard parent as reference to allele coding. If the reference is not provided, the function codes 2 the allele with major frequency and 0 the minor allele, such that the association studies can compute interaction between subpopulation and minor allele.

Examples

# NOT RUN {
data(tpod)
gen=reference(gen=gen,ref=NULL)
# }