BGGE

A R package to prepare datasets and fit GE genomic models

Installation

To complete installation of BGGE, you have to install a few packages first.

install.packages("devtools")
devtools::install_github('italo-granato/BGGE')

Simple use

library(BGGE)
library(BGLR)
data(wheat)

X <- scale(wheat.X, scale = TRUE, center = TRUE)
rownames(X) <- 1:599
pheno_geno <- data.frame(env = gl(n = 4, k = 599), 
                         GID = gl(n=599, k=1, length = 599*4),
                         value = as.vector(wheat.Y))

# Creating kernel for GE model

K <- getK(Y = pheno_geno, X = X, kernel = "GB", model = "MM")
y <- as.vector(wheat.Y)

fit <- BGGE(y = y, K = K, ne = rep(599, 4))

Others params

params
XF Design matrix for fixed effects.
ite Number of iterations.
ne Number of subjects by environment.
burn Number of iterations to be discarded as burn-in.
thin Thinin interval.
verbose Should report be printed on screen?
tol tolerance for zero. Default is 1e-10

Authors

Italo Granato Jaime D. Cuevas D. Francisco J. Luna-Vázquez

https://www.dropbox.com/sh/1aezkhn359b3yx8/AAC8XbERcAW5ZPDfHlpspJs0a?dl=0