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  "Title": "Create Custom Plots for Viewing Genetic Association Results",
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  "Description": "A collection of functions for visualizing,exploring and\nannotating genetic association results.Association results from\nmultiple traits can be viewed simultaneously along with gene\nannotation, over the entire genome (Manhattan plot) or in the\nmore detailed regional view.",
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    "effectplot",
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    "foresttopr",
    "get_best_snp_per_MB",
    "get_gene",
    "get_gene_coords",
    "get_genes_by_Gene_Symbol",
    "get_genes_in_region",
    "get_lead_snps",
    "get_overlapping_snps_by_pos",
    "get_sign_and_sugg_loci",
    "get_snps_within_region",
    "get_snpset",
    "get_snpset_code",
    "get_top_snp",
    "get_topr_colors",
    "get_topr_old_colors",
    "locuszoom",
    "manhattan",
    "manhattanExtra",
    "match_alleles",
    "match_by_alleles",
    "match_by_pos",
    "qqtopr",
    "regionplot"
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      "title": "Finngen r7 Crohn‘s disease (K11_CROHNS)",
      "object": "CD_FINNGEN",
      "class": [
        "data.frame"
      ],
      "fields": [
        "CHROM",
        "POS",
        "REF",
        "ALT",
        "P",
        "BETA",
        "ID",
        "AF"
      ],
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      "table": true,
      "tojson": true
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      "title": "UKBB Crohns disease (ICD 10 code K50)",
      "object": "CD_UKBB",
      "class": [
        "data.frame"
      ],
      "fields": [
        "CHROM",
        "POS",
        "ID",
        "REF",
        "ALT",
        "P",
        "OR",
        "AF"
      ],
      "rows": 21717,
      "table": true,
      "tojson": true
    },
    {
      "name": "R2_CD_UKBB",
      "title": "Example dataset including the R2 column for the locuszoom plot function",
      "object": "R2_CD_UKBB",
      "class": [
        "data.frame"
      ],
      "fields": [
        "CHROM",
        "POS",
        "ID",
        "P",
        "R2"
      ],
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      "table": true,
      "tojson": true
    },
    {
      "name": "UC_UKBB",
      "title": "UKBB Ulcerative colitis (ICD 10 code K51)",
      "object": "UC_UKBB",
      "class": [
        "data.frame"
      ],
      "fields": [
        "CHROM",
        "POS",
        "ID",
        "REF",
        "ALT",
        "P",
        "OR",
        "AF"
      ],
      "rows": 45012,
      "table": true,
      "tojson": true
    }
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  "_help": [
    {
      "page": "annotate_with_nearest_gene",
      "title": "Get the nearest gene for one or more snps",
      "topics": [
        "annotate_with_nearest_gene"
      ]
    },
    {
      "page": "CD_FINNGEN",
      "title": "Finngen r7 Crohn‘s disease (K11_CROHNS)",
      "topics": [
        "CD_FINNGEN"
      ]
    },
    {
      "page": "CD_UKBB",
      "title": "UKBB Crohns disease (ICD 10 code K50)",
      "topics": [
        "CD_UKBB"
      ]
    },
    {
      "page": "create_snpset",
      "title": "Create a dataframe that can be used as input for making effect plots",
      "topics": [
        "create_snpset"
      ]
    },
    {
      "page": "create_snpset_code",
      "title": "Show the code/functions used to create a snpset",
      "topics": [
        "create_snpset_code"
      ]
    },
    {
      "page": "effect_plot",
      "title": "Create a plot comparing effects within two datasets",
      "topics": [
        "effect_plot"
      ]
    },
    {
      "page": "effectplot",
      "title": "Create a plot comparing variant effects in two datasets",
      "topics": [
        "effectplot"
      ]
    },
    {
      "page": "flip_to_positive_allele_for_dat1",
      "title": "Flip to the positive allele for dataset 1",
      "topics": [
        "flip_to_positive_allele_for_dat1"
      ]
    },
    {
      "page": "foresttopr",
      "title": "Create a forest plot from one or more association result tables",
      "topics": [
        "foresttopr"
      ]
    },
    {
      "page": "get_best_snp_per_MB",
      "title": "Get the index/lead variants",
      "topics": [
        "get_best_snp_per_MB"
      ]
    },
    {
      "page": "get_gene",
      "title": "Get the genetic position of a gene by gene name",
      "topics": [
        "get_gene"
      ]
    },
    {
      "page": "get_gene_coords",
      "title": "Get the genetic position of a gene by gene name",
      "topics": [
        "get_gene_coords"
      ]
    },
    {
      "page": "get_genes_by_Gene_Symbol",
      "title": "Get the genetic position of a gene by its gene name",
      "topics": [
        "get_genes_by_Gene_Symbol"
      ]
    },
    {
      "page": "get_genes_in_region",
      "title": "Get SNPs/variants within region",
      "topics": [
        "get_genes_in_region"
      ]
    },
    {
      "page": "get_lead_snps",
      "title": "Get the index/lead variants",
      "topics": [
        "get_lead_snps"
      ]
    },
    {
      "page": "get_overlapping_snps_by_pos",
      "title": "Get variants that overlap between two datasets",
      "topics": [
        "get_overlapping_snps_by_pos"
      ]
    },
    {
      "page": "get_sign_and_sugg_loci",
      "title": "Get the index/lead variants",
      "topics": [
        "get_sign_and_sugg_loci"
      ]
    },
    {
      "page": "get_snps_within_region",
      "title": "Get SNPs/variants within region",
      "topics": [
        "get_snps_within_region"
      ]
    },
    {
      "page": "get_snpset",
      "title": "Create a dataframe that can be used as input for making effect plots",
      "topics": [
        "get_snpset"
      ]
    },
    {
      "page": "get_snpset_code",
      "title": "Show the code/functions used to get a snpset",
      "topics": [
        "get_snpset_code"
      ]
    },
    {
      "page": "get_top_snp",
      "title": "Get the top hit from the dataframe",
      "topics": [
        "get_top_snp"
      ]
    },
    {
      "page": "get_topr_colors",
      "title": "Get the topr custom colors",
      "topics": [
        "get_topr_colors"
      ]
    },
    {
      "page": "get_topr_old_colors",
      "title": "Get the topr custom colors from v. 2.0.2",
      "topics": [
        "get_topr_old_colors"
      ]
    },
    {
      "page": "locuszoom",
      "title": "Create a locuszoom-like plot",
      "topics": [
        "locuszoom"
      ]
    },
    {
      "page": "manhattan",
      "title": "Create a Manhattan plot",
      "topics": [
        "manhattan"
      ]
    },
    {
      "page": "manhattanExtra",
      "title": "Create a Manhattan plot highlighting genome-wide significant and suggestive loci",
      "topics": [
        "manhattanExtra"
      ]
    },
    {
      "page": "match_alleles",
      "title": "Match the variants in the snpset by their alleles",
      "topics": [
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      ]
    },
    {
      "page": "match_by_alleles",
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      "topics": [
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    },
    {
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      "title": "Get variants that overlap between two datasets",
      "topics": [
        "match_by_pos"
      ]
    },
    {
      "page": "qqtopr",
      "title": "Create a quantile quantile (QQ) plot",
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        "qqtopr"
      ]
    },
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      "page": "R2_CD_UKBB",
      "title": "Example dataset including the R2 column for the locuszoom plot function",
      "topics": [
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      ]
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      "page": "regionplot",
      "title": "Create a regionplot",
      "topics": [
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      ]
    },
    {
      "page": "UC_UKBB",
      "title": "UKBB Ulcerative colitis (ICD 10 code K51)",
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      ]
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