Changes:
- Added compatibility with the functions (print() and plot()).
- Include ORCID of the authors.
- Include url of the project.
- Now the
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.
- Italo Granato (Author, Maintainer)
- Jaime D. Cuevas D. (Author)
- Francisco J. Luna-Vázquez (Author, Maintainer)
