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  "Package": "PolyHaplotyper",
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  "Title": "Assignment of Haplotypes Based on SNP Dosages in Diploids and\nPolyploids",
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  "Author": "Roeland E. Voorrips",
  "Maintainer": "Roeland E. Voorrips <roeland.voorrips@wur.nl>",
  "Description": "Infer the genetic composition of individuals in terms of\nhaplotype dosages for a haploblock, based on bi-allelic marker\ndosages, for any ploidy level. Reference: Voorrips and Tumino:\nPolyHaplotyper: haplotyping in polyploids based on bi-allelic\nmarker dosage data. Submitted to BMC Bioinformatics (2021).",
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  "Repository": "https://polyploids.r-universe.dev",
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    "allhap",
    "allHaplotypes",
    "build_ahccompletelist",
    "calcMrkHaptable",
    "calcStatistics",
    "checkmrkDosage",
    "compareHapMrkDosages",
    "compareHapresults",
    "expandHapdos",
    "getFSfreqs",
    "getGameteFreqs",
    "hapcomb2hapdos",
    "hapdos2hapcomb",
    "hapdos2mrkdos",
    "haploblock_df2list",
    "inferHaplotypes",
    "make.Happyinf.input",
    "make.SATlotyper.input",
    "make.ShesisPlus.input",
    "mergeReplicates",
    "mrkdid2mrkdos",
    "mrkdos2mrkdid",
    "overviewByFS",
    "padded",
    "pedigreeHapCheck",
    "pedigreeSim2PH",
    "read.Happyinf.output",
    "read.SATlotyper.output",
    "read.ShesisPlus.output",
    "run.SATlotyper",
    "showOneFS",
    "totHapcombCount",
    "usedhap"
  ],
  "_datasets": [
    {
      "name": "demo_ped",
      "title": "pedigree",
      "object": "PolyHaplotyper_demo",
      "class": [
        "data.frame"
      ],
      "fields": [
        "genotype",
        "mother",
        "father",
        "sample_nr"
      ],
      "rows": 661,
      "table": true,
      "tojson": true
    },
    {
      "name": "demo_snpdos",
      "title": "dosages of SNP alleles",
      "object": "PolyHaplotyper_demo",
      "class": [
        "data.frame"
      ],
      "fields": [],
      "rows": 30,
      "table": true,
      "tojson": true
    },
    {
      "name": "phblocks",
      "title": "List of markers per haploblock",
      "object": "PolyHaplotyper_small",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "phdos",
      "title": "dosages of SNP alleles",
      "object": "PolyHaplotyper_small",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [],
      "rows": 8,
      "table": true,
      "tojson": true
    },
    {
      "name": "phFS",
      "title": "members of FS families",
      "object": "PolyHaplotyper_small",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "phpar",
      "title": "parents of FS families",
      "object": "PolyHaplotyper_small",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [],
      "rows": 4,
      "table": true,
      "tojson": true
    },
    {
      "name": "phped",
      "title": "pedigree",
      "object": "PolyHaplotyper_small",
      "class": [
        "data.frame"
      ],
      "fields": [
        "genotype",
        "mother",
        "father"
      ],
      "rows": 661,
      "table": true,
      "tojson": true
    },
    {
      "name": "phresults",
      "title": "haplotyping results",
      "object": "PolyHaplotyper_small",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "allhap",
      "title": "Find all possible haplotypes",
      "topics": [
        "allhap"
      ]
    },
    {
      "page": "allHaplotypes",
      "title": "get all haplotypes for the given markers",
      "topics": [
        "allHaplotypes"
      ]
    },
    {
      "page": "build_ahccompletelist",
      "title": "generate a list with all haplotype combinations",
      "topics": [
        "build_ahccompletelist"
      ]
    },
    {
      "page": "calcMrkHaptable",
      "title": "produce a table of nr of markers vs nr of haplotypes",
      "topics": [
        "calcMrkHaptable"
      ]
    },
    {
      "page": "calcStatistics",
      "title": "calculate some statistics of the solutions of all haploblocks",
      "topics": [
        "calcStatistics"
      ]
    },
    {
      "page": "checkmrkDosage",
      "title": "check a marker dosages matrix or data.frame",
      "topics": [
        "checkmrkDosage"
      ]
    },
    {
      "page": "compareHapMrkDosages",
      "title": "compare haplotyping results with observed markers dosages",
      "topics": [
        "compareHapMrkDosages"
      ]
    },
    {
      "page": "compareHapresults",
      "title": "compare two haplotyping results",
      "topics": [
        "compareHapresults"
      ]
    },
    {
      "page": "demo_ped",
      "title": "pedigree",
      "topics": [
        "demo_ped"
      ]
    },
    {
      "page": "demo_snpdos",
      "title": "dosages of SNP alleles",
      "topics": [
        "demo_snpdos"
      ]
    },
    {
      "page": "expandHapdos",
      "title": "Add dropped rows back to haplotype dosage matrix",
      "topics": [
        "expandHapdos"
      ]
    },
    {
      "page": "getFSfreqs",
      "title": "get all FS haplotype combinations expected from two parental haplotype combinations, with their frequencies",
      "topics": [
        "getFSfreqs"
      ]
    },
    {
      "page": "getGameteFreqs",
      "title": "get all gametes and their frequencies for a parental haplotype combination",
      "topics": [
        "getGameteFreqs"
      ]
    },
    {
      "page": "hapcomb2hapdos",
      "title": "convert haplotype combinations to haplotype dosages",
      "topics": [
        "hapcomb2hapdos"
      ]
    },
    {
      "page": "hapdos2hapcomb",
      "title": "convert haplotype dosages to haplotype combinations",
      "topics": [
        "hapdos2hapcomb"
      ]
    },
    {
      "page": "hapdos2mrkdos",
      "title": "calculate the marker dosages resulting from haplotype dosage combinations",
      "topics": [
        "hapdos2mrkdos"
      ]
    },
    {
      "page": "haploblock_df2list",
      "title": "convert a haploblock-defining data frame to a list",
      "topics": [
        "haploblock_df2list"
      ]
    },
    {
      "page": "inferHaplotypes",
      "title": "infer haplotypes for one or more haploblocks",
      "topics": [
        "inferHaplotypes"
      ]
    },
    {
      "page": "make.Happyinf.input",
      "title": "convert PolyHaplotyper input data to Happy-inf format",
      "topics": [
        "make.Happyinf.input"
      ]
    },
    {
      "page": "make.SATlotyper.input",
      "title": "convert PolyHaplotyper marker data to SATlotyper format",
      "topics": [
        "make.SATlotyper.input"
      ]
    },
    {
      "page": "make.ShesisPlus.input",
      "title": "convert PolyHaplotyper marker data to ShesisPlus format",
      "topics": [
        "make.ShesisPlus.input"
      ]
    },
    {
      "page": "mergeReplicates",
      "title": "merge replicate samples in dosage matrix",
      "topics": [
        "mergeReplicates"
      ]
    },
    {
      "page": "mrkdid2mrkdos",
      "title": "get the marker dosages from mrkdids (marker dosage IDs)",
      "topics": [
        "mrkdid2mrkdos"
      ]
    },
    {
      "page": "mrkdos2mrkdid",
      "title": "get marker dosage IDs from marker dosages",
      "topics": [
        "mrkdos2mrkdid"
      ]
    },
    {
      "page": "overviewByFS",
      "title": "generate an overview of the results by haploblock and by FS family",
      "topics": [
        "overviewByFS"
      ]
    },
    {
      "page": "padded",
      "title": "pad an integer (prefix with zeroes to a fixed length)",
      "topics": [
        "padded"
      ]
    },
    {
      "page": "pedigreeHapCheck",
      "title": "check the consistency of haploblock genotypes over a pedigree",
      "topics": [
        "pedigreeHapCheck"
      ]
    },
    {
      "page": "pedigreeSim2PH",
      "title": "convert the PedigreeSim true haplotypes to marker dosages and haplotype dosages",
      "topics": [
        "pedigreeSim2PH"
      ]
    },
    {
      "page": "phblocks",
      "title": "List of markers per haploblock",
      "topics": [
        "phblocks"
      ]
    },
    {
      "page": "phdos",
      "title": "dosages of SNP alleles",
      "topics": [
        "phdos"
      ]
    },
    {
      "page": "phFS",
      "title": "members of FS families",
      "topics": [
        "phFS"
      ]
    },
    {
      "page": "phpar",
      "title": "parents of FS families",
      "topics": [
        "phpar"
      ]
    },
    {
      "page": "phped",
      "title": "pedigree",
      "topics": [
        "phped"
      ]
    },
    {
      "page": "phresults",
      "title": "haplotyping results",
      "topics": [
        "phresults"
      ]
    },
    {
      "page": "read.Happyinf.output",
      "title": "read the haplotyping results from the Happy-inf output",
      "topics": [
        "read.Happyinf.output"
      ]
    },
    {
      "page": "read.SATlotyper.output",
      "title": "read the haplotyping results from the SATlotyper output",
      "topics": [
        "read.SATlotyper.output"
      ]
    },
    {
      "page": "read.ShesisPlus.output",
      "title": "Read the haplotyping results from the ShesisPlus output",
      "topics": [
        "read.ShesisPlus.output"
      ]
    },
    {
      "page": "run.SATlotyper",
      "title": "A simple interface to run SATlotyper",
      "topics": [
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      ]
    },
    {
      "page": "showOneFS",
      "title": "show marker and haplotype dosages for one FS family",
      "topics": [
        "showOneFS"
      ]
    },
    {
      "page": "totHapcombCount",
      "title": "calculate the total nr of possible haplotype combinations",
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    },
    {
      "page": "usedhap",
      "title": "Find all used (inferred) haplotypes",
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      ]
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