{
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  "Package": "vcfR",
  "Title": "Manipulate and Visualize VCF Data",
  "Description": "Facilitates easy manipulation of variant call format (VCF)\ndata. Functions are provided to rapidly read from and write to\nVCF files. Once VCF data is read into R a parser function\nextracts matrices of data. This information can then be used\nfor quality control or other purposes. Additional functions\nprovide visualization of genomic data. Once processing is\ncomplete data may be written to a VCF file (*.vcf.gz). It also\nmay be converted into other popular R objects (e.g., genlight,\nDNAbin). VcfR provides a link between VCF data and familiar R\nsoftware.",
  "Version": "1.16.0",
  "Authors@R": "c(\nperson(c(\"Brian\", \"J.\"), \"Knaus\", role = c(\"cre\", \"aut\"),\nemail = \"briank.lists@gmail.com\", comment = c(ORCID = \"0000-0003-1665-4343\")),\nperson(c(\"Niklaus\", \"J.\"), \"Grunwald\", role = \"aut\",\nemail = \"grunwaln@science.oregonstate.edu\", comment = c(ORCID = \"0000-0003-1656-7602\")),\nperson(c(\"Eric\", \"C.\"), \"Anderson\", role = \"ctb\",\nemail = \"eric.anderson@noaa.gov\", comment = c(ORCID = \"0000-0003-1326-0840\")),\nperson(c(\"David\", \"J.\"), \"Winter\", role = \"ctb\",\nemail = \"david.winter@gmail.com\"),\nperson(c(\"Zhian\", \"N.\"), \"Kamvar\", role = \"ctb\",\nemail = \"zkamvar@gmail.com\", comment = c(ORCID = \"0000-0003-1458-7108\")),\nperson(c(\"Javier\", \"F.\"), \"Tabima\", role = \"ctb\",\nemail = \"caifaz01@gmail.com\", comment = c(ORCID = \"0000-0002-3603-2691\"))\n)",
  "Maintainer": "Brian J. Knaus <briank.lists@gmail.com>",
  "URL": "https://github.com/knausb/vcfR,\nhttps://knausb.github.io/vcfR_documentation/",
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  "Author": "Brian J. Knaus [cre, aut] (ORCID:\n<https://orcid.org/0000-0003-1665-4343>), Niklaus J. Grunwald\n[aut] (ORCID: <https://orcid.org/0000-0003-1656-7602>), Eric C.\nAnderson [ctb] (ORCID:\n<https://orcid.org/0000-0003-1326-0840>), David J. Winter\n[ctb], Zhian N. Kamvar [ctb] (ORCID:\n<https://orcid.org/0000-0003-1458-7108>), Javier F. Tabima\n[ctb] (ORCID: <https://orcid.org/0000-0002-3603-2691>)",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2026-02-23 18:10:02 UTC",
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  "_exports": [
    "%>%",
    "AD_frequency",
    "addID",
    "alleles2consensus",
    "ann2chromR",
    "check_keys",
    "chromo",
    "chromoqc",
    "chromR2vcfR",
    "create.chromR",
    "dr.plot",
    "extract_gt_tidy",
    "extract_info_tidy",
    "extract.gt",
    "extract.haps",
    "extract.indels",
    "extract.info",
    "freq_peak",
    "freq_peak_plot",
    "genetic_diff",
    "get.alleles",
    "getALT",
    "getCHROM",
    "getFILTER",
    "getFIX",
    "getID",
    "getINFO",
    "getPOS",
    "getQUAL",
    "getREF",
    "gt.to.popsum",
    "gt2popsum",
    "head",
    "heatmap.bp",
    "INFO2df",
    "is_het",
    "is.biallelic",
    "is.het",
    "is.indel",
    "is.polymorphic",
    "maf",
    "masker",
    "masplit",
    "metaINFO2df",
    "NM2winNM",
    "nrow",
    "null.plot",
    "ordisample",
    "pairwise_genetic_diff",
    "peak_to_ploid",
    "plot",
    "print",
    "proc.chromR",
    "queryMETA",
    "rank.variants.chromR",
    "rbind2",
    "read.vcfR",
    "regex.win",
    "rePOS",
    "seq2chromR",
    "seq2rects",
    "var.win",
    "variant.table",
    "vcf_field_names",
    "vcfR2chromR",
    "vcfR2DNAbin",
    "vcfR2genind",
    "vcfR2genlight",
    "vcfR2hapmap",
    "vcfR2loci",
    "vcfR2migrate",
    "vcfR2tidy",
    "win.table",
    "windowize.NM",
    "write.fasta",
    "write.var.info",
    "write.vcf",
    "write.win.info",
    "z.score"
  ],
  "_datasets": [
    {
      "name": "chrom",
      "title": "Example chromR object.",
      "object": "chromR_example",
      "file": "chromR_example.RData",
      "class": [
        "chromR"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "dna",
      "title": "Example data for vcfR.",
      "object": "vcfR_example",
      "file": "vcfR_example.rdata",
      "class": [
        "DNAbin"
      ],
      "fields": {},
      "rows": 1,
      "table": false,
      "tojson": false
    },
    {
      "name": "gff",
      "title": "Example data for vcfR.",
      "object": "vcfR_example",
      "file": "vcfR_example.rdata",
      "class": [
        "data.frame"
      ],
      "fields": [
        "V1",
        "V2",
        "V3",
        "V4",
        "V5",
        "V6",
        "V7",
        "V8",
        "V9"
      ],
      "rows": 23,
      "table": true,
      "tojson": true
    },
    {
      "name": "vcf",
      "title": "Example data for vcfR.",
      "object": "vcfR_example",
      "file": "vcfR_example.rdata",
      "class": [
        "vcfR"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "vcfR_test",
      "title": "Test data for vcfR.",
      "object": "vcfR_test",
      "file": "vcfR_test.RData",
      "class": [
        "vcfR"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "vep",
      "title": "Example data from the Variant Effect Predictor (VEP).",
      "object": "vep",
      "file": "vep.RData",
      "class": [
        "vcfR"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "AD_frequency",
      "title": "AD_frequency",
      "topics": [
        "AD_frequency"
      ]
    },
    {
      "page": "addID",
      "title": "Populate the ID column of VCF data",
      "topics": [
        "addID"
      ]
    },
    {
      "page": "check_keys",
      "title": "Check that INFO and FORMAT keys are unique",
      "topics": [
        "check_keys"
      ]
    },
    {
      "page": "chromo_plot",
      "title": "Plot chromR object",
      "topics": [
        "chromo",
        "chromoqc",
        "chromo_plot"
      ]
    },
    {
      "page": "chromR_functions",
      "title": "chromR_functions",
      "topics": [
        "chromR functions",
        "masker",
        "variant.table",
        "win.table"
      ]
    },
    {
      "page": "chromR_example",
      "title": "Example chromR object.",
      "topics": [
        "chrom",
        "chromR_example"
      ]
    },
    {
      "page": "chromR-class",
      "title": "chromR class",
      "topics": [
        "chromR-class"
      ]
    },
    {
      "page": "chrom_to_vcfR",
      "title": "Convert chrom objects to vcfR objects",
      "topics": [
        "chromR2vcfR"
      ]
    },
    {
      "page": "vcfR_to_tidy_conversion",
      "title": "Convert vcfR objects to tidy data frames",
      "topics": [
        "Convert to tidy data frames",
        "extract_gt_tidy",
        "extract_info_tidy",
        "vcfR2tidy",
        "vcf_field_names"
      ]
    },
    {
      "page": "create_chromR",
      "title": "Create chromR object",
      "topics": [
        "ann2chromR",
        "create.chromR",
        "seq2chromR",
        "vcf2chromR",
        "vcfR2chromR"
      ]
    },
    {
      "page": "drplot",
      "title": "dr.plot elements",
      "topics": [
        "dr.plot",
        "dr.plot elements",
        "null.plot"
      ]
    },
    {
      "page": "extract_gt",
      "title": "Extract elements from vcfR objects",
      "topics": [
        "extract.gt",
        "extract.haps",
        "extract.indels",
        "extract.info",
        "is.indel"
      ]
    },
    {
      "page": "vcfR_conversion",
      "title": "Convert vcfR objects to other formats",
      "topics": [
        "Format conversion",
        "vcfR2genind",
        "vcfR2genlight",
        "vcfR2loci"
      ]
    },
    {
      "page": "freq_peak",
      "title": "freq_peak",
      "topics": [
        "freq_peak"
      ]
    },
    {
      "page": "freq_peak_plot",
      "title": "Plot freq_peak object",
      "topics": [
        "freq_peak_plot"
      ]
    },
    {
      "page": "genetic_diff",
      "title": "Genetic differentiation",
      "topics": [
        "genetic_diff"
      ]
    },
    {
      "page": "genotype_matrix",
      "title": "Genotype matrix functions",
      "topics": [
        "alleles2consensus",
        "Genotype matrix functions",
        "get.alleles"
      ]
    },
    {
      "page": "getFIX",
      "title": "Get elements from the fixed region of a VCF file",
      "topics": [
        "getALT",
        "getALT,chromR-method",
        "getALT,vcfR-method",
        "getCHROM",
        "getCHROM,chromR-method",
        "getCHROM,vcfR-method",
        "getFILTER",
        "getFILTER,chromR-method",
        "getFILTER,vcfR-method",
        "getFIX",
        "getFIX,chromR-method",
        "getFIX,vcfR-method",
        "getID",
        "getID,chromR-method",
        "getID,vcfR-method",
        "getINFO",
        "getINFO,chromR-method",
        "getINFO,vcfR-method",
        "getPOS",
        "getPOS,chromR-method",
        "getPOS,vcfR-method",
        "getQUAL",
        "getQUAL,chromR-method",
        "getQUAL,vcfR-method",
        "getREF",
        "getREF,chromR-method",
        "getREF,vcfR-method"
      ]
    },
    {
      "page": "pop_gen_sum",
      "title": "Population genetics summaries",
      "topics": [
        "gt.to.popsum",
        "gt2popsum",
        "Population genetics summaries"
      ]
    },
    {
      "page": "heatmap_bp",
      "title": "Heatmap with barplots",
      "topics": [
        "heatmap.bp"
      ]
    },
    {
      "page": "INFO2df",
      "title": "Reformat INFO data as a data.frame",
      "topics": [
        "INFO2df",
        "metaINFO2df"
      ]
    },
    {
      "page": "is_het",
      "title": "Query genotypes for heterozygotes",
      "topics": [
        "is.het",
        "is_het"
      ]
    },
    {
      "page": "maf",
      "title": "Minor allele frequency",
      "topics": [
        "maf"
      ]
    },
    {
      "page": "masplit",
      "title": "masplit",
      "topics": [
        "masplit"
      ]
    },
    {
      "page": "ordisample",
      "title": "Ordinate a sample's data",
      "topics": [
        "ordisample"
      ]
    },
    {
      "page": "pairwise_genetic_diff",
      "title": "Pairwise genetic differentiation across populations",
      "topics": [
        "pairwise_genetic_diff"
      ]
    },
    {
      "page": "peak_to_ploid",
      "title": "Convert allele balance peaks to ploidy",
      "topics": [
        "peak_to_ploid"
      ]
    },
    {
      "page": "proc_chromR",
      "title": "Process chromR object",
      "topics": [
        "proc.chromR",
        "Process chromR objects",
        "regex.win",
        "seq2rects",
        "var.win"
      ]
    },
    {
      "page": "query_gt",
      "title": "Query the gt slot",
      "topics": [
        "is.biallelic",
        "is.polymorphic",
        "is_biallelic",
        "query.gt"
      ]
    },
    {
      "page": "queryMETA",
      "title": "Query the META section of VCF data",
      "topics": [
        "queryMETA"
      ]
    },
    {
      "page": "ranking",
      "title": "Ranking variants within windows",
      "topics": [
        "rank.variants.chromR",
        "Ranking"
      ]
    },
    {
      "page": "rePOS",
      "title": "Create non-overlapping positions (POS) for VCF data",
      "topics": [
        "rePOS"
      ]
    },
    {
      "page": "chromR-method",
      "title": "chromR-method",
      "topics": [
        "chromR,chromR-method",
        "head,chromR-method",
        "length,chromR-method",
        "names<-,chromR,character-method",
        "plot,chromR-method",
        "print,chromR-method",
        "show,chromR-method"
      ]
    },
    {
      "page": "vcfR-method",
      "title": "show",
      "topics": [
        "dim,vcfR-method",
        "dim.vcfR",
        "head",
        "head,vcfR-method",
        "nrow,vcfR-method",
        "nrow.vcfR",
        "plot,vcfR-method",
        "rbind2,vcfR,ANY-method",
        "rbind2,vcfR,missing-method",
        "rbind2,vcfR,vcfR-method",
        "rbind2.vcfR",
        "show,vcfR-method",
        "[,vcfR,ANY,ANY,ANY-method",
        "[,vcfR-method"
      ]
    },
    {
      "page": "io_vcfR",
      "title": "Read and write vcf format files",
      "topics": [
        "read.vcfR",
        "VCF input and output",
        "write.vcf"
      ]
    },
    {
      "page": "vcfR_example",
      "title": "Example data for vcfR.",
      "topics": [
        "dna",
        "gff",
        "vcf",
        "vcfR_example"
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      "page": "vcfR2DNAbin",
      "title": "Convert vcfR to DNAbin",
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      "topics": [
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      "page": "vep",
      "title": "Example data from the Variant Effect Predictor (VEP).",
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      "source": "converting_data.Rmd",
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      "author": "Brian J. Knaus",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Data import",
        "Creating *.vcf.gz format files.",
        "Creating genind objects",
        "Creating genclone objects",
        "Creating genlight objects",
        "Creating snpclone objects",
        "Creating DNAbin objects",
        "Creating loci objects",
        "Conclusion"
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      "headings": [
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        "The fix region",
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      "created": "2017-01-07 16:45:08",
      "modified": "2020-01-10 09:50:03",
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