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  "Title": "Genotype Quality Control with 'PLINK'",
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    "check_hwe",
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    "check_relatedness",
    "check_sex",
    "check_snp_missingness",
    "checkFiltering",
    "checkLoadingMat",
    "checkPlink",
    "checkPlink2",
    "checkRF_path",
    "cleanData",
    "convert_from_vcf",
    "convert_to_plink2",
    "evaluate_ancestry_prediction",
    "evaluate_check_het_and_miss",
    "evaluate_check_relatedness",
    "evaluate_check_sex",
    "overviewPerIndividualQC",
    "overviewPerMarkerQC",
    "perIndividualQC",
    "perMarkerQC",
    "pruning_ld",
    "relatednessFilter",
    "rename_variant_identifiers",
    "run_ancestry_format",
    "run_ancestry_prediction",
    "run_check_heterozygosity",
    "run_check_missingness",
    "run_check_relatedness",
    "run_check_sex",
    "testNumerics"
  ],
  "_help": [
    {
      "page": "ancestry_prediction",
      "title": "Predicting sample superpopulation ancestry",
      "topics": [
        "ancestry_prediction"
      ]
    },
    {
      "page": "check_het_and_miss",
      "title": "Identification of individuals with outlying missing genotype or heterozygosity rates",
      "topics": [
        "check_het_and_miss"
      ]
    },
    {
      "page": "check_hwe",
      "title": "Identification of SNPs showing a significant deviation from Hardy-Weinberg- equilibrium (HWE)",
      "topics": [
        "check_hwe"
      ]
    },
    {
      "page": "check_maf",
      "title": "Identification of SNPs with low minor allele frequency",
      "topics": [
        "check_maf"
      ]
    },
    {
      "page": "check_relatedness",
      "title": "Identification of related individuals",
      "topics": [
        "check_relatedness"
      ]
    },
    {
      "page": "check_sex",
      "title": "Identification of individuals with discordant sex information",
      "topics": [
        "check_sex"
      ]
    },
    {
      "page": "check_snp_missingness",
      "title": "Identification of SNPs with high missingness rate",
      "topics": [
        "check_snp_missingness"
      ]
    },
    {
      "page": "checkFiltering",
      "title": "Check and construct PLINK sample and marker filters",
      "topics": [
        "checkFiltering"
      ]
    },
    {
      "page": "checkLoadingMat",
      "title": "Checking the path of the loading matrix",
      "topics": [
        "checkLoadingMat"
      ]
    },
    {
      "page": "checkPlink",
      "title": "Check PLINK software access",
      "topics": [
        "checkPlink"
      ]
    },
    {
      "page": "checkPlink2",
      "title": "Check PLINK2 software access",
      "topics": [
        "checkPlink2"
      ]
    },
    {
      "page": "checkRemoveIDs",
      "title": "Check and construct individual IDs to be removed",
      "topics": [
        "checkRemoveIDs"
      ]
    },
    {
      "page": "checkRF_path",
      "title": "Checking the path of userinputted random forest",
      "topics": [
        "checkRF_path"
      ]
    },
    {
      "page": "cleanData",
      "title": "Create plink dataset with individuals and markers passing quality control",
      "topics": [
        "cleanData"
      ]
    },
    {
      "page": "convert_from_vcf",
      "title": "Converting VCF data files into PLINK v1.9 and PLINK v2.0 data files",
      "topics": [
        "convert_from_vcf"
      ]
    },
    {
      "page": "convert_to_plink2",
      "title": "Converting PLINK v1.9 data files into PLINK v2.0 data files",
      "topics": [
        "convert_to_plink2"
      ]
    },
    {
      "page": "evaluate_ancestry_prediction",
      "title": "Predicting sample superpopulation ancestry",
      "topics": [
        "evaluate_ancestry_prediction"
      ]
    },
    {
      "page": "evaluate_check_het_and_miss",
      "title": "Evaluate results from PLINK missing genotype and heterozygosity rate check.",
      "topics": [
        "evaluate_check_het_and_miss"
      ]
    },
    {
      "page": "evaluate_check_relatedness",
      "title": "Evaluate results from PLINK IBD estimation.",
      "topics": [
        "evaluate_check_relatedness"
      ]
    },
    {
      "page": "evaluate_check_sex",
      "title": "Evaluate results from PLINK sex check.",
      "topics": [
        "evaluate_check_sex"
      ]
    },
    {
      "page": "overviewPerIndividualQC",
      "title": "Overview of per sample QC",
      "topics": [
        "overviewPerIndividualQC"
      ]
    },
    {
      "page": "overviewPerMarkerQC",
      "title": "Overview of per marker QC",
      "topics": [
        "overviewPerMarkerQC"
      ]
    },
    {
      "page": "perIndividualQC",
      "title": "Quality control for all individuals in plink-dataset",
      "topics": [
        "perIndividualQC"
      ]
    },
    {
      "page": "perMarkerQC",
      "title": "Quality control for all markers in plink-dataset",
      "topics": [
        "perMarkerQC"
      ]
    },
    {
      "page": "pruning_ld",
      "title": "Pruning of SNPs in Linkage Disequilibrium",
      "topics": [
        "pruning_ld"
      ]
    },
    {
      "page": "relatednessFilter",
      "title": "Remove related individuals while keeping maximum number of individuals",
      "topics": [
        "relatednessFilter"
      ]
    },
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      "page": "rename_variant_identifiers",
      "title": "Renaming variants",
      "topics": [
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    },
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      "title": "Running functions to format data for ancestry prediction",
      "topics": [
        "run_ancestry_format"
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    },
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      "title": "Projecting the study data set onto the PC space of the reference dataset",
      "topics": [
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    },
    {
      "page": "run_check_heterozygosity",
      "title": "Run PLINK heterozygosity rate calculation",
      "topics": [
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      ]
    },
    {
      "page": "run_check_missingness",
      "title": "Run PLINK missingness rate calculation",
      "topics": [
        "run_check_missingness"
      ]
    },
    {
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      "title": "Run PLINK IBD estimation",
      "topics": [
        "run_check_relatedness"
      ]
    },
    {
      "page": "run_check_sex",
      "title": "Run PLINK sexcheck",
      "topics": [
        "run_check_sex"
      ]
    },
    {
      "page": "testNumerics",
      "title": "Test lists for different properties of numerics",
      "topics": [
        "testNumerics"
      ]
    }
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