Genomic Selection

The GS is a r-package that has been created to run cross validation using BGLR - sommer packages. This allows you run CV by command line or with a user interface in shiny.

Installation

devtools::install_github("AparicioJohan/GS")

or …

source("https://install-github.me/AparicioJohan/GS")

library(GS)

Run the Shiny app

There’s only one exported function in the package and it runs the Shiny app:

GS::GS_shiny()

Command line

The code below shows how you can run the cross validation.

# library(sommer)
# data(DT_cpdata)
#
# geno <- GT_cpdata
# samp <- rownames(GT_cpdata)
# phen <- DT_cpdata
#
# crossGP(geno, samp, phen, prior = "sommer", niter=2, testporc = 0.3, traits = names(phen)[5])

#---------------------

# geno <- "D:/OneDrive - CGIAR/2020/imputed_rrBLUP.in"
# samp <- "D:/OneDrive - CGIAR/2020/imputed_rrBLUP_samples.txt"
# phen <- "D:/OneDrive - CGIAR/2020/Phenotypic_Analysis.csv"
#
# crossGP(geno,samp,phen,prior = "sommer", niter=2,testporc = 0.3,traits = "Pal13C_drt")