1. Improved techniques for sampling complex pedigrees with the Gibbs sampler
- Author
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Fernando Rohan L, Totir Liviu R, and Abraham K Joseph
- Subjects
Gibbs sampler ,Markov chain Monte Carlo ,pedigree peeling ,Elston Stewart algorithm ,Animal culture ,SF1-1100 ,Genetics ,QH426-470 - Abstract
Abstract Markov chain Monte Carlo (MCMC) methods have been widely used to overcome computational problems in linkage and segregation analyses. Many variants of this approach exist and are practiced; among the most popular is the Gibbs sampler. The Gibbs sampler is simple to implement but has (in its simplest form) mixing and reducibility problems; furthermore in order to initiate a Gibbs sampling chain we need a starting genotypic or allelic configuration which is consistent with the marker data in the pedigree and which has suitable weight in the joint distribution. We outline a procedure for finding such a configuration in pedigrees which have too many loci to allow for exact peeling. We also explain how this technique could be used to implement a blocking Gibbs sampler.
- Published
- 2007
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