make_grm: Function to make genomic relation matrices

In wolfemd/alphaSimHlpR: Functions added to AlphaSimR to simplify simulating breeding schemes

Description

Function to make a genomic relationship matrix to be used to analyze the phenotypic records. So far only works with parentSelCritGEBV and popImprovementByParentSel.

Usage

make_grm(records, indivs2keep, bsp, SP, grmType = "add")

Arguments

records	The breeding program records object. See fillPipeline for details
indivs2keep	chr. vector of id's to be included in the grm. Must be present in c(records$F1,bsp$checks).
bsp	The breeding scheme parameter list
SP	The AlphaSimR SimParam object. Needed to pull the SNP genotypes

Details

Setting up to distinguish between parent and cross selection and additive and non-additive predictions. Uses genomicMateSelectR functions, which will need to be installed for these to work.

This version uses the genomicMateSelectR::kinship.

Includes a new grmType param, can produce additive and dominance matrices. Same matrix as A.mat by default grmType="add".

records maintains the phenotypic and genotypic records across years and stages. For GEBV analysis, you need the GRM of these individuals. makeGRM assumes the first phenotyping stage (records[[2]]) has all individuals that have been phenotyped. The GRM also includes the unphenotyped new F1 individuals in records[[1]]

Value

A genomic relationship matrix

wolfemd/alphaSimHlpR documentation built on Sept. 19, 2021, 6:25 p.m.