Irreducibility and efficiency of ESIP to sample marker genotypes in large pedigrees with loops

dc.contributor.author Ferhandez, Soledad
dc.contributor.author Fernando, Rohan
dc.contributor.author Carriquiry, Alicia
dc.contributor.author Gulbrandtsen, Bernt
dc.contributor.author Stricker, Christian
dc.contributor.author Schelling, Matthias
dc.contributor.author Carriquiry, Alicia
dc.contributor.department Statistics
dc.date 2018-02-17T06:10:15.000
dc.date.accessioned 2020-07-02T06:57:04Z
dc.date.available 2020-07-02T06:57:04Z
dc.date.copyright Tue Jan 01 00:00:00 UTC 2002
dc.date.issued 2002-01-01
dc.description.abstract <p>Markov chain Monte Carlo (MCMC) methods have been proposed to overcome computational problems in linkage and segregation analyses. This approach involves sampling genotypes at the marker and trait loci. Among MCMC methods, scalar-Gibbs is the easiest to implement, and it is used in genetics. However, the Markov chain that corresponds to scalar- Gibbs may not be irreducible when the marker locus has more than two alleles, and even when the chain is irreducible, mixing has been observed to be slow. Joint sampling of genotypes has been proposed as a strategy to overcome these problems. An algorithm that combines the Elston-Stewart algorithm and iterative peeling (ESIP sampler) to sample genotypes jointly from the entire pedigree is used in this study. Here, it is shown that the ESIP sampler yields an irreducible Markov chain, regardless of the number of alleles at a locus. Further, results obtained by ESIP sampler are compared with other methods in the literature. Of the methods that are guaranteed to be irreducible, ESIP was the most efficient.</p>
dc.description.comments <p>This article is from <em>Genetics Selection Evolution </em>34 (2002): 537. Posted with permission.</p>
dc.format.mimetype application/pdf
dc.identifier archive/lib.dr.iastate.edu/stat_las_pubs/19/
dc.identifier.articleid 1019
dc.identifier.contextkey 7849157
dc.identifier.s3bucket isulib-bepress-aws-west
dc.identifier.submissionpath stat_las_pubs/19
dc.identifier.uri https://dr.lib.iastate.edu/handle/20.500.12876/90498
dc.language.iso en
dc.source.bitstream archive/lib.dr.iastate.edu/stat_las_pubs/19/2002_CarriquiryAL_IrreducibilityEfficiencyESIP.pdf|||Fri Jan 14 21:49:54 UTC 2022
dc.subject.disciplines Animal Sciences
dc.subject.disciplines Statistics and Probability
dc.subject.keywords Metropolis-Hasting
dc.subject.keywords irreducibility
dc.subject.keywords Elston-Stewart algorithm
dc.subject.keywords iterative peeling
dc.title Irreducibility and efficiency of ESIP to sample marker genotypes in large pedigrees with loops
dc.type article
dc.type.genre article
dspace.entity.type Publication
relation.isAuthorOfPublication 6ddd5891-2ad0-4a93-89e5-8c35c28b0de4
relation.isOrgUnitOfPublication 264904d9-9e66-4169-8e11-034e537ddbca
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