| Type: | Package |
| Title: | Genomic Prediction of Hybrid Performance with Graphical User Interface |
| Version: | 2.1 |
| Description: | Performs genomic prediction of hybrid performance using eight GS methods including GBLUP, BayesB, RKHS, PLS, LASSO, Elastic net, XGBoost and LightGBM. GBLUP: genomic best liner unbiased prediction, RKHS: reproducing kernel Hilbert space, PLS: partial least squares regression, LASSO: least absolute shrinkage and selection operator, XGBoost: extreme gradient boosting, LightGBM: light gradient boosting machine. It also provides fast cross-validation and mating design scheme for training population (Xu S et al (2016) <doi:10.1111/tpj.13242>; Xu S (2017) <doi:10.1534/g3.116.038059>). |
| License: | GPL-3 |
| Encoding: | UTF-8 |
| LazyData: | true |
| RoxygenNote: | 7.3.2 |
| Depends: | R (≥ 4.1.0) |
| Imports: | shiny, data.table, DT, predhy(≥ 2.1.2), BGLR, pls, glmnet, xgboost, lightgbm, foreach, doParallel, parallel, htmltools |
| NeedsCompilation: | no |
| Packaged: | 2025-04-14 19:32:34 UTC; YuxiangZhang |
| Repository: | CRAN |
| Date/Publication: | 2025-04-14 19:50:05 UTC |
| Author: | Yang Xu [aut], Guangning Yu [aut], Yuxiang Zhang [aut, cre], Yanru Cui [ctb], Shizhong Xu [ctb], Chenwu Xu [ctb] |
| Maintainer: | Yuxiang Zhang <yuxiangzhang_99@foxmail.com> |
Phenotypic data of hybrids
Description
This dataset contains phenotypic data of 410 hybrids for grain yield in maize.
Usage
hybrid_phe
Format
A data frame with 410 rows and 3 variables:
MThe names of male parents.
FThe names of female parents.
GYThe grain yield of hybrids.
Genotype in Hapmap Format
Description
Genotypic data of 348 maize inbred lines in Hapmap format with double bit.
Usage
input_geno
Format
A data frame with 4979 rows and 359 columns.
Genotype in Numeric Format
Description
Genotypic data of 50 rice inbred lines with 1000 SNPs.
Usage
input_geno1
Format
A data frame with 1000 rows and 50 variables.
Graphical User Interface for R package predhy
Description
Graphical User Interface for cross validation, genotype conversion and hybrid performance prediction.
Usage
predhy.GUI()
Value
No return value, called for Graphical User Interface
Examples
{
predhy.GUI()}