SNP-BLUP and GBLUP
by Filippo Biscarini
We begin here a series of posts with the aim to clarify the SNP-BLUP and GBLUP approaches to the prediction of response (targets) variables from SNP genotype data:
- the two models and their equivalency/interchangeability
- how cross-validation apply to these two parameterizations of (essentially) the same problem
- applications in R
Outline of the material
- Super-quick recap of linear mixed models
- Application of mixed models to genetics and breeding: from BLUP to GBLUP
- An alternative (yet equivalent) parameterization: the SNP-BLUP
- How to do cross-validation with SNP-BLUP
- How to do cross-validation with GBLUP