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Haplotype Estimation from Fuzzy Genotypes Using Penalized Likelihood
The Composite Link Model is a generalization of the generalized linear model in which expected values of observed counts are constructed as a sum of generalized linear components. When combined with penalized likelihood, it provides a powerful and elegant way to estimate haplotype probabilities from...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3169573/ https://www.ncbi.nlm.nih.gov/pubmed/21931662 http://dx.doi.org/10.1371/journal.pone.0024219 |
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author | Uh, Hae-Won Eilers, Paul H. C. |
author_facet | Uh, Hae-Won Eilers, Paul H. C. |
author_sort | Uh, Hae-Won |
collection | PubMed |
description | The Composite Link Model is a generalization of the generalized linear model in which expected values of observed counts are constructed as a sum of generalized linear components. When combined with penalized likelihood, it provides a powerful and elegant way to estimate haplotype probabilities from observed genotypes. Uncertain (“fuzzy”) genotypes, like those resulting from AFLP scores, can be handled by adding an extra layer to the model. We describe the model and the estimation algorithm. We apply it to a data set of accurate human single nucleotide polymorphism (SNP) and to a data set of fuzzy tomato AFLP scores. |
format | Online Article Text |
id | pubmed-3169573 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-31695732011-09-19 Haplotype Estimation from Fuzzy Genotypes Using Penalized Likelihood Uh, Hae-Won Eilers, Paul H. C. PLoS One Research Article The Composite Link Model is a generalization of the generalized linear model in which expected values of observed counts are constructed as a sum of generalized linear components. When combined with penalized likelihood, it provides a powerful and elegant way to estimate haplotype probabilities from observed genotypes. Uncertain (“fuzzy”) genotypes, like those resulting from AFLP scores, can be handled by adding an extra layer to the model. We describe the model and the estimation algorithm. We apply it to a data set of accurate human single nucleotide polymorphism (SNP) and to a data set of fuzzy tomato AFLP scores. Public Library of Science 2011-09-08 /pmc/articles/PMC3169573/ /pubmed/21931662 http://dx.doi.org/10.1371/journal.pone.0024219 Text en Uh and Eilers. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Uh, Hae-Won Eilers, Paul H. C. Haplotype Estimation from Fuzzy Genotypes Using Penalized Likelihood |
title | Haplotype Estimation from Fuzzy Genotypes Using Penalized Likelihood |
title_full | Haplotype Estimation from Fuzzy Genotypes Using Penalized Likelihood |
title_fullStr | Haplotype Estimation from Fuzzy Genotypes Using Penalized Likelihood |
title_full_unstemmed | Haplotype Estimation from Fuzzy Genotypes Using Penalized Likelihood |
title_short | Haplotype Estimation from Fuzzy Genotypes Using Penalized Likelihood |
title_sort | haplotype estimation from fuzzy genotypes using penalized likelihood |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3169573/ https://www.ncbi.nlm.nih.gov/pubmed/21931662 http://dx.doi.org/10.1371/journal.pone.0024219 |
work_keys_str_mv | AT uhhaewon haplotypeestimationfromfuzzygenotypesusingpenalizedlikelihood AT eilerspaulhc haplotypeestimationfromfuzzygenotypesusingpenalizedlikelihood |