NAM (version 1.0.2.2)

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 intead 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.

Examples

data(tpod)
gen=reference(gen=gen,ref=NULL)