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 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')
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)
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