calc_gmat: Calculate Realized Genomic Relationship Matrices

In etnite/bwardr: Brian Ward personal R package

Calculate Realized Genomic Relationship Matrices

Description

Calculate Realized Genomic Relationship Matrices

Usage

calc_gmat(data, method = "GOF")

Arguments

data	Dataframe or matrix with individuals in rows and markers in columns. Markers should be encoded in minor-allele dosage format (i.e. 0 = homozygous for major allele, 1 = heterozygous, 2 = homozygous for minor allele).
method	String to select the method to use for calculating the relationship matrix. Available methods are: "GOF" - observed allele frequencies (VanRaden, 2008) "GD" - weighted markers by recipricals of expected variance (Forni et al., 2011) "G05" - allele frequencies fixed at 0.5 (Forni et al., 2011) "GM" - allele frequencies fixed at mean for each locus (Forni et al., 2011)

Details

This function is adapted from an example from Chapter 11 of Genetic Data Analysis for Plant and Animal Breeding, by Isik, Holland and Maltecca, 2017 (DOI 10.1007/978-3-319-55177-7). However, their code is more complex, as it includes one additional computation method that uses observed pedigree data, and it outputs both realized genetic and additive relationships. This function only returns the realized genetic relationship matrix.

Value

The full realized genetic relationship matrix (G)

etnite/bwardr documentation built on Jan. 6, 2023, 7:12 a.m.