{
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  "Package": "genetics",
  "Title": "Population Genetics",
  "Version": "1.3.8.1.3",
  "Date": "2012-11-26",
  "Author": "Gregory Warnes, with contributions from Gregor Gorjanc,\nFriedrich Leisch, and Michael Man.",
  "Maintainer": "Gregory Warnes <greg@warnes.net>",
  "Description": "Classes and methods for handling genetic data. Includes\nclasses to represent genotypes and haplotypes at single markers\nup to multiple markers on multiple chromosomes. Function\ninclude allele frequencies, flagging homo/heterozygotes,\nflagging carriers of certain alleles, estimating and testing\nfor Hardy-Weinberg disequilibrium, estimating and testing for\nlinkage disequilibrium, ...",
  "biocViews": "Genetics",
  "License": "GPL",
  "Packaged": {
    "Date": "2026-07-12 07:44:39 UTC",
    "User": "root"
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  "NeedsCompilation": "no",
  "Repository": "https://warnes.r-universe.dev",
  "Date/Publication": "2021-03-01 06:10:07 UTC",
  "RemoteUrl": "https://github.com/cran/genetics",
  "RemoteRef": "HEAD",
  "RemoteSha": "b96215a2ce0d9bac40f63d5747fb5f0efca2ce80",
  "_user": "warnes",
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  "_created": "2026-07-12T07:44:39.000Z",
  "_published": "2026-07-12T07:48:57.271Z",
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    },
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      "date": "2013-09-03"
    },
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    },
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      "date": "2019-04-22"
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  ],
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    "allele",
    "allele.count",
    "allele.names",
    "as.factor",
    "as.genotype",
    "as.genotype.allele.count",
    "as.haplotype",
    "carrier",
    "ci.balance",
    "diseq",
    "diseq.ci",
    "expectedGenotypes",
    "expectedHaplotypes",
    "gene",
    "gene<-",
    "geno.as.array",
    "genotype",
    "genotypeOrder",
    "genotypeOrder<-",
    "getgene",
    "getlocus",
    "getmarker",
    "gregorius",
    "groupGenotype",
    "hap",
    "hapambig",
    "hapenum",
    "hapfreq",
    "haplotype",
    "hapmcmc",
    "hapshuffle",
    "heterozygote",
    "homozygote",
    "HWE.chisq",
    "HWE.exact",
    "HWE.test",
    "is.gene",
    "is.genotype",
    "is.haplotype",
    "is.locus",
    "is.marker",
    "LD",
    "LDplot",
    "LDtable",
    "locus",
    "locus<-",
    "makeGenotypes",
    "makeHaplotypes",
    "marker",
    "marker<-",
    "mourant",
    "nallele",
    "order",
    "power.casectrl",
    "shortsummary.genotype",
    "summary.LD.data.frame",
    "write.marker.file",
    "write.pedigree.file",
    "write.pop.file"
  ],
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      "name": "gregorius",
      "title": "Probability of Observing All Alleles with a Given Frequency in a Sample of a Specified Size.",
      "object": "gregorius",
      "file": "gregorius.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "minfreq",
        "sigma05",
        "sigma01",
        "sigma001"
      ],
      "rows": 16,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "ci.balance",
      "title": "Experimental Function to Correct Confidence Intervals At or Near Boundaries of the Parameter Space by 'Sliding' the Interval on the Quantile Scale.",
      "topics": [
        "ci.balance"
      ]
    },
    {
      "page": "depreciated",
      "title": "Depreciated functions",
      "topics": [
        "power.casectrl"
      ]
    },
    {
      "page": "diseq",
      "title": "Estimate or Compute Confidence Interval for the Single-Marker Disequilibrium",
      "topics": [
        "diseq",
        "diseq.ci",
        "diseq.genotype",
        "diseq.table",
        "print.diseq"
      ]
    },
    {
      "page": "expectedGenotypes",
      "title": "Construct expected genotypes/haplotypes according to known allele variants",
      "topics": [
        "expectedGenotypes",
        "expectedHaplotypes"
      ]
    },
    {
      "page": "genotype",
      "title": "Genotype or Haplotype Objects.",
      "topics": [
        "%in%",
        "%in%.default",
        "%in%.genotype",
        "%in%.haplotype",
        "==.genotype",
        "==.haplotype",
        "allele.count.genotype",
        "as.genotype",
        "as.genotype.allele.count",
        "as.genotype.character",
        "as.genotype.default",
        "as.genotype.factor",
        "as.genotype.genotype",
        "as.genotype.haplotype",
        "as.genotype.table",
        "as.haplotype",
        "genotype",
        "haplotype",
        "heterozygote.genotype",
        "homozygote.genotype",
        "is.genotype",
        "is.haplotype",
        "nallele",
        "print.allele.count",
        "print.allele.genotype",
        "print.genotype",
        "[.genotype",
        "[.haplotype",
        "[<-.genotype",
        "[<-.haplotype"
      ]
    },
    {
      "page": "gregorius",
      "title": "Probability of Observing All Alleles with a Given Frequency in a Sample of a Specified Size.",
      "topics": [
        "gregorius"
      ]
    },
    {
      "page": "groupGenotype",
      "title": "Group genotype values",
      "topics": [
        "groupGenotype"
      ]
    },
    {
      "page": "homozygote",
      "title": "Extract Features of Genotype objects",
      "topics": [
        "allele",
        "allele.count",
        "allele.names",
        "carrier",
        "carrier.genotype",
        "heterozygote",
        "homozygote"
      ]
    },
    {
      "page": "HWE.chisq",
      "title": "Perform Chi-Square Test for Hardy-Weinberg Equilibrium",
      "topics": [
        "HWE.chisq",
        "HWE.chisq.genotype"
      ]
    },
    {
      "page": "HWE.exact",
      "title": "Exact Test of Hardy-Weinberg Equilibrium for 2-Allele Markers",
      "topics": [
        "HWE.exact"
      ]
    },
    {
      "page": "HWE.test",
      "title": "Estimate Disequilibrium and Test for Hardy-Weinberg Equilibrium",
      "topics": [
        "HWE.test",
        "HWE.test.data.frame",
        "HWE.test.genotype",
        "print.HWE.test"
      ]
    },
    {
      "page": "LD",
      "title": "Pairwise linkage disequilibrium between genetic markers.",
      "topics": [
        "LD",
        "LD.data.frame",
        "LD.genotype"
      ]
    },
    {
      "page": "locus",
      "title": "Create and Manipulate Locus, Gene, and Marker Objects",
      "topics": [
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        "as.character.locus",
        "as.character.marker",
        "gene",
        "gene<-",
        "getgene",
        "getlocus",
        "getmarker",
        "is.gene",
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        "locus",
        "locus<-",
        "marker",
        "marker<-",
        "print.gene",
        "print.locus",
        "print.marker"
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    },
    {
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      "topics": [
        "makeGenotypes",
        "makeHaplotypes"
      ]
    },
    {
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      "title": "Order/sort genotype/haplotype object",
      "concept": [
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        "sort.haplotype"
      ],
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        "genotypeOrder<-",
        "order",
        "order.genotype",
        "sort.genotype"
      ]
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      "title": "Plot genotype object",
      "topics": [
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      ]
    },
    {
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      "title": "Textual and graphical display of linkage disequilibrium (LD) objects",
      "topics": [
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        "LDtable",
        "plot.LD.data.frame",
        "print.LD",
        "print.LD.data.frame",
        "print.summary.LD.data.frame",
        "summary.LD.data.frame"
      ]
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    {
      "page": "summary.genotype",
      "title": "Allele and Genotype Frequency from a Genotype or Haplotype Object",
      "topics": [
        "print.summary.genotype",
        "summary.genotype"
      ]
    },
    {
      "page": "undocumented",
      "title": "Undocumented functions",
      "topics": [
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        "as.factor",
        "as.factor.allele.genotype",
        "as.factor.default",
        "as.factor.genotype",
        "geno.as.array",
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        "mknum",
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    },
    {
      "page": "write.pop.file",
      "title": "Create genetics data files",
      "topics": [
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        "write.pedigree.file",
        "write.pop.file"
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