{
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  "Package": "isoRelate",
  "Title": "Identity-by-Descent Inference of Haploid Recombining Organisms",
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  "Authors@R": "person(\"Lyndal\", \"Henden\", email = \"lyndal_henden@hotmail.com\", role = c(\"aut\", \"cre\"))",
  "Description": "Pairwise identity by descent inference of haploid species\nusing single nucleotide polymorphism data. isoRelate can detect\nIBD in the presence of multi-clonal infections and also\nprovides a function for identifying loci under recent positive\nselection.",
  "License": "MIT + file LICENSE",
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  "Repository": "https://plasmogenepi.r-universe.dev",
  "Date/Publication": "2018-03-19 05:48:43 UTC",
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  "Author": "Lyndal Henden [aut, cre]",
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    "plotIBDproportions",
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      ],
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      "tojson": true
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      "page": "AmatrixDD",
      "title": "The matrix A in the equation Ax=b for 2 diploid chromosomes",
      "topics": [
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      ]
    },
    {
      "page": "AmatrixHD",
      "title": "The matrix A in the equation Ax=b for 1 haploid and 1 diploid chromosome",
      "topics": [
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      ]
    },
    {
      "page": "AmatrixHH",
      "title": "The matrix A in the equation Ax=b for 2 haploid chromosomes",
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      "page": "annotation_genes",
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      "page": "areColors",
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      "topics": [
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    },
    {
      "page": "bVectorDD",
      "title": "The vector b in the equation Ax=b for 2 diploid chromosomes",
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      "page": "bVectorHH",
      "title": "The vector b in the equation Ax=b for 2 haploid chromosomes",
      "topics": [
        "bVectorHH"
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    },
    {
      "page": "calculateAlpha",
      "title": "Calculate alpha",
      "topics": [
        "calculateAlpha"
      ]
    },
    {
      "page": "calculateBeta",
      "title": "Calculate beta",
      "topics": [
        "calculateBeta"
      ]
    },
    {
      "page": "calculateGamma",
      "title": "Calculate gamma",
      "topics": [
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      ]
    },
    {
      "page": "calculateLogLikelihood",
      "title": "Calculate the log-likelihood of the data",
      "topics": [
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    },
    {
      "page": "calculateMeiosis",
      "title": "Estimation of Meiosis",
      "topics": [
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    },
    {
      "page": "calculateMissingness",
      "title": "Calculate Missingness Proportions",
      "topics": [
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    },
    {
      "page": "calculatePopAlleleFreq",
      "title": "Calculate Allele Frequencies for SNPs from Genotype Data",
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      "title": "Calculate scale",
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      "page": "calculateViterbi",
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      "page": "genotypeErrorD",
      "title": "The genotyping error probability for 1 diploid chromosome",
      "topics": [
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      "title": "The genotyping error probability for 1 haploid chromosome",
      "topics": [
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      "page": "getColourPaletteMajor",
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      "topics": [
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    },
    {
      "page": "getColourPaletteMinor",
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      "topics": [
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    },
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      "title": "Pre-Analysis Data Processing",
      "topics": [
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    },
    {
      "page": "getIBDiclusters",
      "title": "Interval Cluster Networks",
      "topics": [
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    },
    {
      "page": "getIBDiR",
      "title": "Selection Significance Statistic",
      "topics": [
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    },
    {
      "page": "getIBDmatrix",
      "title": "Binary IBD Matrix",
      "topics": [
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    },
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      "page": "getIBDparameters",
      "title": "Parameter Estimation",
      "topics": [
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    },
    {
      "page": "getIBDpclusters",
      "title": "Genome Cluster Networks",
      "topics": [
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    },
    {
      "page": "getIBDposterior",
      "title": "IBD Posterior Probabilities",
      "topics": [
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    },
    {
      "page": "getIBDproportion",
      "title": "Proportion of Pairs IBD",
      "topics": [
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    },
    {
      "page": "getIBDsegments",
      "title": "IBD Segment Detection",
      "topics": [
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    },
    {
      "page": "getIBDsummary",
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      "topics": [
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    },
    {
      "page": "getOverlap",
      "title": "function to find IBD that overlap interval",
      "topics": [
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    },
    {
      "page": "groupPairs",
      "title": "Group Combinations for Analysis",
      "topics": [
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    },
    {
      "page": "haplotypeToGenotype",
      "title": "Call Genotypes from Haplotype Data",
      "topics": [
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    {
      "page": "highlight_genes",
      "title": "Plasmodium Falciparum Gene Highlight Dataset",
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      "page": "IBDLabel",
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      "page": "IBDMatrix",
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      "topics": [
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      "page": "IBDparameters",
      "title": "IBDparameters() calculates IBD probabilities then estimates the number of meiosis for an isolate pair.",
      "topics": [
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      "page": "IBDTable",
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      "topics": [
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      "page": "iRfunction",
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      "page": "isolatePairs",
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      "page": "merge_lists",
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      "page": "my_ibd",
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    {
      "page": "plotIBDclusters",
      "title": "Plot Cluster Networks",
      "topics": [
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    {
      "page": "plotIBDiR",
      "title": "Plot iR Statistics",
      "topics": [
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    },
    {
      "page": "plotIBDproportions",
      "title": "Plot The Proportion of Pairs IBD",
      "topics": [
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    },
    {
      "page": "plotIBDsegments",
      "title": "Plot IBD Segments",
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    },
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      "page": "png_genotypes",
      "title": "Filtered Genotypes For The Papua New Guinea Dataset",
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    {
      "page": "png_ibd",
      "title": "IBD Segments For The Papua New Guinea Dataset",
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      "title": "Papua New Guinea Plasmodium Falciparum Dataset",
      "topics": [
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    {
      "page": "roundDecimal",
      "title": "Round digits to specified decimal places",
      "topics": [
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      "page": "transitionProbDD",
      "title": "The transition probabilities for 2 diploid chromosomes",
      "topics": [
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      "page": "transitionProbHD",
      "title": "The transition probabilities for 1 haploid and 1 diploid chromosome",
      "topics": [
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    {
      "page": "transitionProbHH",
      "title": "The transition probabilities for 2 haploid chromosomes",
      "topics": [
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    {
      "page": "trueGenotypes",
      "title": "Matrices of all possible genotype combinations between pairs, given MOI",
      "topics": [
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