GEmetrics (version 1.0.0)

BGLR_format: Format the phenotypic response matrix for BGLR

Description

This function formats the phenotypic data as well as the kinship matrix for BGLR

Usage

BGLR_format(Pheno, K)

Value

a list of two elements: a "BGLR_pheno" phenotypic response matrix with J columns to be used in BGLR and the corresponding "BGLR_K" kinship matrix.

Arguments

Pheno

a data frame with three columns: "Y" for phenotypic values, "Genotype" for genotype names and "Environment" for environment names. All genotypes names must be included in the set or row/column names of the "K" matrix. The number of environments (J) must be at least two

K

a square kinship or genomic relationship matrix for N genotypes whose row and column names include those of the "Genotype" column of the "Pheno" matrix

Examples

## Set seed for reproductibility
set.seed(123)

## Load "wheat" dataset from BGLR
data("wheat",package = "BGLR")

## Generate a design data frame for all genotypes in 5 environments
Design <- expand.grid(Genotype=rownames(wheat.A),Environment=paste0("Env",1:5))

## Set sparseness by discarding 75% of the combinations
Design <- Design[-sample(nrow(Design),round(nrow(Design)*3/4)),]

## Simulate phenotypic data with default parameter values
DataSim <- Simulate_MET_data(Design=Design,K=wheat.A)

## Generate the phenotypic response matrix for BGLR and the corresponding kinship matrix
BGLR_data <- BGLR_format(Pheno=DataSim$Pheno,K=wheat.A)
head(BGLR_data$BGLR_pheno)