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        "mother",
        "father",
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        "age"
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      "title": "Simulated data on 10 families with approximately 100 members each",
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        "indiv",
        "mother",
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        "aff",
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        "geno"
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      "page": "clipp-package",
      "title": "clipp: Calculate Likelihoods by Pedigree Paring",
      "topics": [
        "clipp-package",
        "clipp"
      ]
    },
    {
      "page": "combine_loci",
      "title": "Combine the genotype frequencies and transition matrices of two genetic loci",
      "topics": [
        "combine_loci"
      ]
    },
    {
      "page": "dat_large",
      "title": "Simulated data on one family with approximately 10,000 members",
      "topics": [
        "dat_large"
      ]
    },
    {
      "page": "dat_small",
      "title": "Simulated data on 10 families with approximately 100 members each",
      "topics": [
        "dat_small"
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    },
    {
      "page": "geno_freq_monogenic",
      "title": "Calculate genotype frequencies from allele frequencies using Hardy-Weinberg equilibrium",
      "topics": [
        "geno_freq_monogenic"
      ]
    },
    {
      "page": "geno_freq_phased",
      "title": "Calculate phased genotype frequencies from allele frequencies, assuming Hardy-Weinberg equilibrium",
      "topics": [
        "geno_freq_phased"
      ]
    },
    {
      "page": "geno_freq_polygenic",
      "title": "Genotype frequencies for the hypergeometric polygenic model",
      "topics": [
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      ]
    },
    {
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      "title": "Calculate genotype probabilities for a target person",
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      "title": "Calculate the log-likelihoods of pedigrees",
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      "title": "A penetrance matrix relating the phenotypes in 'dat_large' to three genotypes",
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      "title": "A penetrance matrix relating the phenotypes of 'dat_small' to three genotypes",
      "topics": [
        "penet_small"
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    },
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      "page": "trans_monogenic",
      "title": "The transmission matrix for a single genetic locus",
      "topics": [
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      "page": "trans_phased",
      "title": "The transmission matrix for phased genotypes",
      "topics": [
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    },
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      "title": "The transmission matrix for the hypergeometric polygenic model",
      "topics": [
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    }
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      "headings": [
        "Pedigree likelihoods",
        "Specifying the genetic model",
        "Calculating the pedigree likelihood",
        "Maximum likelihood estimation",
        "Incorporating known genotypes",
        "Calculating carrier probabilities",
        "Advanced notes",
        "The Elston-Stewart algorithm",
        "References"
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      "modified": "2022-07-12 04:30:02",
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