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A diplotype is a pair of haplotypes from a given patient – one haplotype comes from mom, and the other comes from dad. A patient has one and only one diplotype. However, as with haplotypes, the lack of knowledge of marker phase makes it necessary to estimate the probability a patient has a given diplotype for a given set of markers. The diplotype table presents a list of all probable diplotypes for all patients, where probable is defined by the EM display threshold. If you wish to only display patients whose diplotype probabilities are over, say, 0.8, then set the EM display threshold to 0.8.

We see in the diplotype type table view that often the diplotype can be assigned with very high probability. This table can be output to other data formats for further analysis, or potentially joined with an existing table of response variables, and then the haplotype or diplotype entries can be used as categorical variables to build models of the response in different haplotype or diplotype subpopulations.