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Haplotype Estimation from Fuzzy Genotypes Using Penalized Likelihood

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  • Hae-Won Uh
  • Paul H C Eilers

Abstract

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.

Suggested Citation

  • Hae-Won Uh & Paul H C Eilers, 2011. "Haplotype Estimation from Fuzzy Genotypes Using Penalized Likelihood," PLOS ONE, Public Library of Science, vol. 6(9), pages 1-9, September.
    • Handle: RePEc:plo:pone00:0024219
    DOI: 10.1371/journal.pone.0024219
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    References listed on IDEAS

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    1. R. Thompson & R. J. Baker, 1981. "Composite Link Functions in Generalized Linear Models," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 30(2), pages 125-131, June.
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