blup_prep: Prepare data for BLUP

In jendelman/StageWise: Two-stage analysis of multi-environment trials for genomic selection and GWAS

Prepare data for BLUP

Description

Prepare data for BLUP

Usage

blup_prep(data, vcov = NULL, geno = NULL, vars, mask = NULL, method = NULL)

Arguments

data	data frame of BLUEs from Stage 1
vcov	list of variance-covariance matrices for the BLUEs
geno	object of class_geno from read_geno
vars	object of class_var from Stage2
mask	(optional) data frame with possible columns "id","env","loc","trait"
method	(optional) "MME", "Vinv", NULL (defaut). see Details

Details

The method argument can be used to control how the linear system is solved. "MME" leads to inversion of the MME coefficient matrix, while "Vinv" leads to inversion of the overall var-cov matrix for the response vector. If NULL, the software uses whichever method involves inverting the smaller matrix. If the number of random effects (m) is less than the number of BLUEs (n), "MME" is used.

For the multi-location model, if all of the environments for a location are masked, the average of the other locations is used when computing average fixed effects.

Value

Object of class_prep

jendelman/StageWise documentation built on Feb. 23, 2025, 11 a.m.