coef.LASSO |
LASSO methods |
coef.SGP |
SGP methods |
cov2cor2 |
Conversion of a covariance matrix to a distance/correlation matrix |
cov2dist |
Conversion of a covariance matrix to a distance/correlation matrix |
fitBLUP |
Fitting a Linear Mixed model to calculate BLUP |
genCOV_xy |
Wheat dataset |
genCOV_yy |
Wheat dataset |
getGenCov |
Pairwise Genetic Covariance |
get_folds |
Data partition into folds of the same size |
LARS |
Least Angle Regression to solve LASSO-type problems |
M |
Wheat dataset |
multitrait.plot |
Accuracy vs penalization from multi-trait SGP |
net |
Graphical Network |
path.plot |
Coefficients path plot |
plot.net |
Plotting a network |
plot.SGP |
Accuracy vs penalization plot |
predict.LASSO |
LASSO methods |
predict.SGP |
SGP methods |
Prune |
R-squared pruning |
readBinary |
Save/read binary files |
read_SGP |
Read and combine SGP outputs |
read_summary |
Read and combine SGP outputs |
resCOV_yy |
Wheat dataset |
saveBinary |
Save/read binary files |
SGP |
Sparse Genomic Prediction |
SGP.CV |
Sparse Genomic Prediction |
solveEN |
Coordinate Descent algorithm to solve Elastic-Net-type problems |
summary.SGP |
SGP methods |
VI_E1 |
Wheat dataset |
wheatHTP |
Wheat dataset |
X_E1 |
Wheat dataset |
Y |
Wheat dataset |