Table 1  Prior density of marker effects, prior variance of marker effects, and suggested formulas for choosing hyperparameter values by model
ModelPrior varianceSolution for scale/variance parameter
Embedded ImageHyperparametersEmbedded Image
Bayesian ridge regression
Embedded ImageEmbedded ImageEmbedded ImageEmbedded Image
Bayesian LASSO
Embedded ImageEmbedded ImageEmbedded ImageEmbedded Image
BayesA
Embedded ImageEmbedded ImageEmbedded ImageEmbedded Image
Spike–slab
Embedded ImageEmbedded ImageEmbedded ImageEmbedded Image
BayesC
Embedded ImageEmbedded ImageEmbedded ImageEmbedded Image
BayesB
Embedded ImageEmbedded ImageEmbedded ImageEmbedded Image
  • Embedded Imagewhere Embedded Image represents number of copies of the allele coded as one at the jth (j = 1,…,p) locus of the ith (i = 1,…,n) individual, and Embedded Image is the average genotype at the jth marker.