Difference between revisions of "HWEP"
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+ | === Derivation === | ||
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+ | Adrian with much help from Hyun. | ||
=== Maintained by === | === Maintained by === | ||
This page is maintained by [mailto:atks@umich.edu Adrian], formulation by Hyun. | This page is maintained by [mailto:atks@umich.edu Adrian], formulation by Hyun. |
Revision as of 13:34, 11 April 2013
Formulation
Hardy Weinberg equilibrium is expected in a panmictic population. The following formulation is a likelihood ratio test statistic that incorporates genotype uncertainty via genotype likelihoods. is the probability of observing the reads for individual assuming that a locus observes HWE. is the probability of observing the reads for individual assuming that a locus does not observe HWE. denotes the genotype composed of alleles and . indexes the individuals from to . is the genotype likelihood. and are the genotype frequencies estimated with and without HWE assumption respectively.
The likelihood ratio test statistic is as follows with degrees of freedom where is the number of alleles.
Derivation
Adrian with much help from Hyun.
Maintained by
This page is maintained by Adrian, formulation by Hyun.