Changes:
BGGE()
function exports the input parameters.See the last updates in NEWS.
To complete installation of dev version of BGGE from GitHub, you must have previously installed the devtools package.
install.packages('devtools')
devtools::install_github('italo/BGGE')
If you want to use the stable version of BGGE package, install it from CRAN.
install.packages('BGGE')
library(BGGE)
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))
fit
## Model Fitted with:
## 1000 Iterations, burning the first 200 and thining every 3
##
## Some predicted Values:
## [1] -0.2737 -0.4081 -0.3799 0.3694 -0.0362 0.2354 0.2840
## [8] -0.1194 -0.7742 -1.0280
##
## Use str() function to found more datailed information.
plot(fit)
| params | Use | | ------- | --------------------------------------------------------------------- | | 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 | | R2 | the proportion of variance expected to be explained by the regression |
First option, by the paper.
@article {Granato2018,
author = {Granato, Italo and Cuevas, Jaime and Luna-V{\'a}zquez, Francisco J. and Crossa, Jos{\'e} and Montesinos-L{\'o}pez, Osval A. and Burgue{\~n}o, Juan and Fritsche-Neto, Roberto},
title = {BGGE: A New Package for Genomic-Enabled Prediction Incorporating Genotype {\texttimes} Environment Interaction Models},
year = {2018},
doi = {10.1534/g3.118.200435},
publisher = {G3: Genes, Genomes, Genetics},
URL = {http://www.g3journal.org/content/early/2018/07/25/g3.118.200435},
eprint = {http://www.g3journal.org/content/early/2018/07/25/g3.118.200435.full.pdf},
journal = {G3: Genes, Genomes, Genetics}
}
Second option, by the package
citation('BGGE')
##
## To cite package 'BGGE' in publications use:
##
## Italo Granato, Luna-Vázquez Francisco J. and Cuevas Jaime
## (2018). BGGE: Bayesian Genomic Linear Models Applied to GE
## Genome Selection. R package version 0.6.5.
## https://github.com/italo-granato/BGGE
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {BGGE: Bayesian Genomic Linear Models Applied to GE Genome Selection},
## author = {Italo Granato and Luna-Vázquez {Francisco J.} and Cuevas Jaime},
## year = {2018},
## note = {R package version 0.6.5},
## url = {https://github.com/italo-granato/BGGE},
## }
If you have any suggestions or feedback, I would love to hear about it. Feel free to report new issues in this link, also if you want to request a feature/report a bug, or make a pull request if you can contribute.
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