Figure 1. The graphical model for the Gibbs sampler.

All variables shown here are involved in updating the information for individual i. Filled-in variables are typically observed, and held constant throughout the run of the sampler. marker alleles that i received from its father and mother. disease locus alleles that i received from its father and mother. , marker and disease locus alleles that individual i passed to its jth offspring. (Only one offspring is shown for illustration.) individual i's phenotype. Selector variable: tells whether i's paternal marker allele comes from its paternal grandfather or grandmother. 's unphased marker genotype. , marker genotype vectors of i's mother and father. If i is a founder, replace by a constant node describing the population allele frequencies. Penetrances = matrix of the probabilities of each phenotype, conditional on disease genotype; held constant.