crossGP returns the cross validation usign differents methodologies as implemented in BGLR, ASReml and sommer package.
crossGP(geno, samp, phen, prior, niter = 50, testporc = 0.3, traits = NULL)
| geno | The name of the file which the genotypic-data are to be read from or a matrix in the r-environment. Data coded as (-1,0,1) |
|---|---|
| samp | The name of the file which the genotypes are to be read from or a vector with the genotype names |
| phen | The name of the file which the phenotypic-data are to be read from or a data.frame in the r-environment. |
| prior | A string vector with some of those models c("ASReml", "RKHS", "sommer", "BRR", "BayesA", "BayesB", "BayesC", "BLasso") |
| niter | A numeric from 0 to 100 |
| testporc | A numeric from 0 to 1 |
| traits | A string vector with the traits names |
list with two elements
# 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")