{
  "_id": "6ac00e7991601a2ad299610a",
  "Package": "RZooRoH",
  "Type": "Package",
  "Title": "Partitioning of Individual Autozygosity into Multiple\nHomozygous-by-Descent Classes",
  "Version": "0.4.2",
  "Authors@R": "c(\nperson(\"Tom\",  \"Druet\", role = c(\"aut\", \"cre\"), email = \"tom.druet@uliege.be\"),\nperson(\"Naveen Kumar\", \"Kadri\", role = \"aut\"),\nperson(\"Natalia\",\"Forneris\",role = \"ctb\"),\nperson(\"Pierre\",\"Faux\",role = \"ctb\"),\nperson(\"Amandine\",\"Bertrand\",role = \"ctb\"),\nperson(\"Mathieu\",\"Gautier\",role = \"aut\"))",
  "Maintainer": "Tom Druet <tom.druet@uliege.be>",
  "Description": "Functions to identify Homozygous-by-Descent (HBD) segments\nassociated with runs of homozygosity (ROH) and to estimate\nindividual autozygosity (or inbreeding coefficient). HBD\nsegments and autozygosity are assigned to multiple HBD classes\nwith a model-based approach relying on a mixture of exponential\ndistributions. The rate of the exponential distribution is\ndistinct for each HBD class and defines the expected length of\nthe HBD segments. This rate is called the \"rate of coancestry\nchange\". The HBD classes are therefore related to the age of\nthe segments (longer segments and smaller rates for recent\nautozygosity / recent common ancestor). The functions allow to\nestimate the parameters of the model (rates of the exponential\ndistributions called also rates of coancestry change; mixing\nproportions related to the inbreeding rate per layer or\ngeneration), to estimate global and local autozygosity\nprobabilities and to identify HBD segments with the Viterbi\ndecoding. Functions also allow to compute identity-by-descent\n(IBD) between pairs of haplotypes, to estimate kinship between\npairs of individuals and to predict inbreeding in the future\nprogeny of a genotyped couple. The current model is fully\ndescribed in Druet and Gautier (2022)\n<doi:10.1016/j.tpb.2022.03.001>. The model and its properties\nwere originally presented in Druet and Gautier (2017)\n<doi:10.1111/mec.14324>. Extension to IBD and kinship analyses\nis described in Forneris et al. (2025)\n<doi:10.1111/1755-0998.14068>.",
  "License": "GPL-3",
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  "Packaged": {
    "Date": "2026-10-02 19:56:50 UTC",
    "User": "root"
  },
  "Author": "Tom Druet [aut, cre], Naveen Kumar Kadri [aut], Natalia\nForneris [ctb], Pierre Faux [ctb], Amandine Bertrand [ctb],\nMathieu Gautier [aut]",
  "Repository": "https://tdruet.r-universe.dev",
  "Date/Publication": "2026-10-02 18:32:24 UTC",
  "RemoteUrl": "https://github.com/cran/RZooRoH",
  "RemoteRef": "HEAD",
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  "_user": "tdruet",
  "_type": "src",
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  "_expires": "2027-01-10T20:05:10.000Z",
  "_created": "2026-10-02T19:56:50.000Z",
  "_published": "2026-10-02T20:05:13.261Z",
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  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/tdruet/actions/runs/37057101258",
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    "author": "Tom Druet <tom.druet@uliege.be>",
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    "message": "version 0.4.2\n",
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  "_mentions": 4,
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  "_topics": [
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  "_rbuild": "4.6.1",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
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  "_realowner": "tdruet",
  "_cranurl": false,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2018-06-19"
    },
    {
      "version": "0.1.1",
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    },
    {
      "version": "0.2.1",
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    {
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      "date": "2019-04-08"
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    {
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    "ComputeFseg",
    "cumhbd",
    "cumkin",
    "merge_kinres",
    "merge_zres",
    "predhbd",
    "probhbd",
    "realized",
    "rohbd",
    "update_kinres",
    "update_zres",
    "zoodata",
    "zookin",
    "zoomodel",
    "zooplot_hbdseg",
    "zooplot_individuals",
    "zooplot_partitioning",
    "zooplot_prophbd",
    "zoorun"
  ],
  "_datasets": [
    {
      "name": "BBB_NMP_ad_subset",
      "title": "Example for \"ad\" format specification",
      "object": "BBB_NMP_ad_subset",
      "class": [
        "data.frame"
      ],
      "fields": [
        "chr",
        "marker_name",
        "pos",
        "allele1",
        "allele2",
        "id1_ad1",
        "id1_ad2",
        "id2_ad1",
        "id2_ad2",
        "id3_ad1",
        "id3_ad2",
        "id4_ad1",
        "id4_ad2",
        "id5_ad1",
        "id5_ad2",
        "id6_ad1",
        "id6_ad2",
        "id7_ad1",
        "id7_ad2",
        "id8_ad1",
        "id8_ad2",
        "id9_ad1",
        "id9_ad2",
        "id10_ad1",
        "id10_ad2"
      ],
      "rows": 1000,
      "table": true,
      "tojson": true
    },
    {
      "name": "BBB_NMP_GP_subset",
      "title": "Example for \"gp\" format specification",
      "object": "BBB_NMP_GP_subset",
      "class": [
        "data.frame"
      ],
      "fields": [
        "chr",
        "marker_name",
        "pos",
        "allele1",
        "allele2",
        "id1_gp1",
        "id1_gp2",
        "id1_gp3",
        "id2_gp1",
        "id2_gp2",
        "id2_gp3",
        "id3_gp1",
        "id3_gp2",
        "id3_gp3",
        "id4_gp1",
        "id4_gp2",
        "id4_gp3",
        "id5_gp1",
        "id5_gp2",
        "id5_gp3",
        "id6_gp1",
        "id6_gp2",
        "id6_gp3",
        "id7_gp1",
        "id7_gp2",
        "id7_gp3",
        "id8_gp1",
        "id8_gp2",
        "id8_gp3",
        "id9_gp1",
        "id9_gp2",
        "id9_gp3",
        "id10_gp1",
        "id10_gp2",
        "id10_gp3"
      ],
      "rows": 1000,
      "table": true,
      "tojson": true
    },
    {
      "name": "BBB_NMP_pl_subset",
      "title": "Example for \"pl\" format specification",
      "object": "BBB_NMP_pl_subset",
      "class": [
        "data.frame"
      ],
      "fields": [
        "chr",
        "marker_name",
        "pos",
        "allele1",
        "allele2",
        "id1_pl1",
        "id1_pl2",
        "id1_pl3",
        "id2_pl1",
        "id2_pl2",
        "id2_pl3",
        "id3_pl1",
        "id3_pl2",
        "id3_pl3",
        "id4_pl1",
        "id4_pl2",
        "id4_pl3",
        "id5_pl1",
        "id5_pl2",
        "id5_pl3",
        "id6_pl1",
        "id6_pl2",
        "id6_pl3",
        "id7_pl1",
        "id7_pl2",
        "id7_pl3",
        "id8_pl1",
        "id8_pl2",
        "id8_pl3",
        "id9_pl1",
        "id9_pl2",
        "id9_pl3",
        "id10_pl1",
        "id10_pl2",
        "id10_pl3"
      ],
      "rows": 1000,
      "table": true,
      "tojson": true
    },
    {
      "name": "BBB_PE_gt_subset",
      "title": "Example for \"gt\" format specification",
      "object": "BBB_PE_gt_subset",
      "class": [
        "data.frame"
      ],
      "fields": [
        "chr",
        "pos",
        "allele1",
        "allele2",
        "id1",
        "id2",
        "id3",
        "id4",
        "id5",
        "id6",
        "id7",
        "id8",
        "id9",
        "id10"
      ],
      "rows": 1000,
      "table": true,
      "tojson": true
    },
    {
      "name": "BBB_samples",
      "title": "A file with names or IDs for ten samples.",
      "object": "BBB_samples",
      "class": [
        "data.frame"
      ],
      "fields": [
        "IDs"
      ],
      "rows": 10,
      "table": true,
      "tojson": true
    },
    {
      "name": "genoex",
      "title": "Subset of a dataset with genotypes for 20 sheeps",
      "object": "genoex",
      "class": [
        "data.frame"
      ],
      "fields": [
        "chr",
        "marker_name",
        "pos",
        "allele1",
        "allele2",
        "id1",
        "id2",
        "id3",
        "id4",
        "id5",
        "id6",
        "id7",
        "id8",
        "id9",
        "id10",
        "id11",
        "id12",
        "id13",
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        "id17",
        "id18",
        "id19",
        "id20"
      ],
      "rows": 14831,
      "table": true,
      "tojson": true
    },
    {
      "name": "genosim",
      "title": "Example from a small simulated data set",
      "object": "genosim",
      "class": [
        "data.frame"
      ],
      "fields": [
        "chr",
        "pos",
        "allele1",
        "allele2",
        "id1",
        "id2",
        "id3",
        "id4",
        "id5",
        "id6",
        "id7",
        "id8",
        "id9",
        "id10",
        "id11",
        "id12",
        "id13",
        "id14",
        "id15",
        "id16",
        "id17",
        "id18",
        "id19",
        "id20"
      ],
      "rows": 10000,
      "table": true,
      "tojson": true
    },
    {
      "name": "hbd1",
      "title": "The result of local IBD probabilities for a pair of individuals among the 18 cows from the Amsterdam Island.",
      "object": "Local_IBD",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "hbd2",
      "title": "The result of local IBD probabilities for a pair of individuals among the 18 cows from the Amsterdam Island (recent only).",
      "object": "Local_IBD",
      "class": [
        "array"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "kintaf_mix4l",
      "title": "The result of a kinship analysis on 18 cattle from the Amsterdam Island.",
      "object": "kintaf_mix4l",
      "class": [
        "kres"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "map1",
      "title": "The map for local IBD probabilities for a pair of individuals among the 18 cows from the Amsterdam Island (recent only).",
      "object": "Local_IBD",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "rara_mix10l",
      "title": "The result of an analysis on 22 sheeps from Rasa Aragonesa population.",
      "object": "rara_mix10l",
      "class": [
        "zres"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "soay_mix10l",
      "title": "The result of an analysis on 110 sheeps from the Soay population.",
      "object": "soay_mix10l",
      "class": [
        "zres"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "typs",
      "title": "Subset of a dataset with genotypes for 6 individuals from a cattle population.",
      "object": "typs",
      "class": [
        "data.frame"
      ],
      "fields": [
        "chr",
        "pos",
        "allele1",
        "allele2",
        "id1",
        "id2",
        "id3",
        "id4",
        "id5",
        "id6"
      ],
      "rows": 6370,
      "table": true,
      "tojson": true
    },
    {
      "name": "typsfrq",
      "title": "A file with marker allele frequencies for the cattle population.",
      "object": "typsfrq",
      "class": [
        "data.frame"
      ],
      "fields": [
        "frq"
      ],
      "rows": 6370,
      "table": true,
      "tojson": true
    },
    {
      "name": "wilt_mix10l",
      "title": "The result of an analysis on 23 sheeps from Wiltshire population.",
      "object": "wilt_mix10l",
      "class": [
        "zres"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "BBB_NMP_ad_subset",
      "title": "Example for \"ad\" format specification",
      "topics": [
        "BBB_NMP_ad_subset"
      ]
    },
    {
      "page": "BBB_NMP_GP_subset",
      "title": "Example for \"gp\" format specification",
      "topics": [
        "BBB_NMP_GP_subset"
      ]
    },
    {
      "page": "BBB_NMP_pl_subset",
      "title": "Example for \"pl\" format specification",
      "topics": [
        "BBB_NMP_pl_subset"
      ]
    },
    {
      "page": "BBB_PE_gt_subset",
      "title": "Example for \"gt\" format specification",
      "topics": [
        "BBB_PE_gt_subset"
      ]
    },
    {
      "page": "BBB_samples",
      "title": "A file with names or IDs for ten samples.",
      "topics": [
        "BBB_samples"
      ]
    },
    {
      "page": "ComputeFseg",
      "title": "Computes inbreeding coefficients based on HBD segments identified with the Viterbi algorithm (similar to a F_ROH estimator), restricted to HBD classes with a rate lower or equal to a chosen threshold T. Returns, per individual, the number of qualifying segments and the corresponding inbreeding coefficient FSEG.",
      "topics": [
        "ComputeFseg"
      ]
    },
    {
      "page": "ComputeFsegAllT",
      "title": "Computes inbreeding coefficients based on HBD segments identified with the Viterbi algorithm (similar to a F_ROH estimator). Returns cumulative inbreeding coefficients estimated using different thresholds corresponding to the rates of the HBD classes.",
      "topics": [
        "ComputeFsegAllT"
      ]
    },
    {
      "page": "cumhbd",
      "title": "Computes the realized inbreeding coefficient",
      "topics": [
        "cumhbd"
      ]
    },
    {
      "page": "cumkin",
      "title": "Computes the realized kinship",
      "topics": [
        "cumkin"
      ]
    },
    {
      "page": "genoex",
      "title": "Subset of a dataset with genotypes for 20 sheeps",
      "topics": [
        "genoex"
      ]
    },
    {
      "page": "genosim",
      "title": "Example from a small simulated data set",
      "topics": [
        "genosim"
      ]
    },
    {
      "page": "hbd1",
      "title": "The result of local IBD probabilities for a pair of individuals among the 18 cows from the Amsterdam Island.",
      "topics": [
        "hbd1"
      ]
    },
    {
      "page": "hbd2",
      "title": "The result of local IBD probabilities for a pair of individuals among the 18 cows from the Amsterdam Island (recent only).",
      "topics": [
        "hbd2"
      ]
    },
    {
      "page": "kintaf_mix4l",
      "title": "The result of a kinship analysis on 18 cattle from the Amsterdam Island.",
      "topics": [
        "kintaf_mix4l"
      ]
    },
    {
      "page": "map1",
      "title": "The map for local IBD probabilities for a pair of individuals among the 18 cows from the Amsterdam Island (recent only).",
      "topics": [
        "map1"
      ]
    },
    {
      "page": "merge_kinres",
      "title": "Merge several kinres objects generated by zookin",
      "topics": [
        "merge_kinres"
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    },
    {
      "page": "merge_zres",
      "title": "Merge several zres objects generated by zoorun",
      "topics": [
        "merge_zres"
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    {
      "page": "predhbd",
      "title": "Extracts the IBD probabilities from the kres object",
      "topics": [
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    {
      "page": "probhbd",
      "title": "Extracts the HBD probabilities from the zres object",
      "topics": [
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    {
      "page": "rara_mix10l",
      "title": "The result of an analysis on 22 sheeps from Rasa Aragonesa population.",
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    },
    {
      "page": "realized",
      "title": "Extracts the realized autozygosity from the zres object",
      "topics": [
        "realized"
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    {
      "page": "rohbd",
      "title": "Extracts the HBD segments from the zres object",
      "topics": [
        "rohbd"
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    },
    {
      "page": "soay_mix10l",
      "title": "The result of an analysis on 110 sheeps from the Soay population.",
      "topics": [
        "soay_mix10l"
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    },
    {
      "page": "typs",
      "title": "Subset of a dataset with genotypes for 6 individuals from a cattle population.",
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    {
      "page": "typsfrq",
      "title": "A file with marker allele frequencies for the cattle population.",
      "topics": [
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    {
      "page": "update_kinres",
      "title": "Update one main kinres object with new results",
      "topics": [
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    {
      "page": "update_zres",
      "title": "Update one main zres object with new results",
      "topics": [
        "update_zres"
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    {
      "page": "wilt_mix10l",
      "title": "The result of an analysis on 23 sheeps from Wiltshire population.",
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    {
      "page": "zoodata",
      "title": "Read the genotype data file",
      "topics": [
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    {
      "page": "zookin",
      "title": "Use the ZooRoH model to estimate kinship between pairs of individuals",
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    {
      "page": "zoomodel",
      "title": "Define the model for the RZooRoH",
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    },
    {
      "page": "zooplot_hbdseg",
      "title": "Plot HBD segments identified with the ZooROH model",
      "topics": [
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    {
      "page": "zooplot_individuals",
      "title": "Plot individual curves with proportion of the genome in each HBD class or cumulated proportion in HBD classes with rates smaller than a threshold.",
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    {
      "page": "zooplot_partitioning",
      "title": "Plot the partitioning of the genome in different HBD classes for each individual",
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    },
    {
      "page": "zooplot_prophbd",
      "title": "Plot proportion of the genome associated with different HBD classes",
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      "title": "Run the ZooRoH model",
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    {
      "source": "zooroh-vignette.Rmd",
      "filename": "zooroh-vignette.html",
      "title": "The RZooRoH package",
      "author": "Tom Druet, Natalia Forneris, Amandine Bertrand, Naveen Kadri & Mathieu Gautier",
      "engine": "knitr::rmarkdown",
      "headings": [
        "1 Installation",
        "2 Citations",
        "3 The multiple HBD classes model",
        "3.1 The hidden Markov model with two classes (HBD vs non-HBD)",
        "3.2 Extending to multiple HBD classes",
        "3.3 Estimating HBD probabilities and identifying HBD segments with an HMM",
        "3.4 Model and results interpretation",
        "4 Differences with other approaches",
        "4.1 Some differences with window-based approaches identifying ROH",
        "4.2 Benefits of using multiple HBD classes",
        "5 Input data",
        "5.1 Input data quality filtering",
        "5.2 Data format and conversion from PED or VCF files",
        "5.2.1 Fields for marker information",
        "5.2.2 Fields for genotype / sequence information",
        "5.2.3 Examples for the six data formats",
        "5.2.4 Converting from ped or VCF files",
        "5.3 Reading the data",
        "5.3.1 Specifying the data file and genotype / sequence format",
        "5.3.2 Specifying the format for marker information",
        "5.3.3 The marker map",
        "5.3.4 Minimal allele frequency threshold",
        "5.3.5 Estimation of alleles frequencies - the EM algorithm",
        "5.3.6 Additional external files (sample names and allele frequencies)",
        "5.3.7 The haploid option",
        "5.3.8 Structure of the zooin object",
        "5.4. Comment on data filtering",
        "6 Defining the model",
        "6.1 Models with one HBD class and one non-HBD class: \\texttt{1L} model",
        "6.2 Models without pre-defined rates: \\texttt{KL} models (\\texttt{RZooRoH} will estimate the rates $R_k$)",
        "6.3 Models with pre-defined rates: \\texttt{MixKL} models",
        "6.3.1 Selecting the number of classes and their rates",
        "6.3.2 Benefits of using pre-defined rates",
        "6.4 Using \\texttt{zoomodel} to define your model",
        "6.4.1 Options",
        "6.4.2 More advanced options: stepfunctions and layers defined as intervals",
        "6.4.2.1 Step functions",
        "6.4.2.2 Layers defined as intervals",
        "6.4.3 Output: the \\texttt{zmodel} object",
        "6.4.4 Some examples of model definition with \\texttt",
        "7 Running \\texttt",
        "7.1 General options",
        "7.2 Parameter estimation",
        "7.2.1 Methods for parameter estimation",
        "7.2.2 Options for parameter estimation",
        "7.2.3 Examples",
        "7.3 Estimating realized autozygosity (with partitioning in different HBD classes)",
        "7.4 Identifying HBD segments",
        "7.5 Estimation of identy-by-descent (IBD) between two phased haplotypes",
        "7.6 More efficient computation when \\texttt",
        "7.7 More examples",
        "7.8 What can be done when 'optim' reports an error for parameter estimation?",
        "7.8 A note on memory usage",
        "8 Description of results",
        "8.1 Parameters (likelihood and convergence)",
        "8.2 Realized autozygosity per class",
        "8.3 Defining inbreeding coefficients (with respect to a base population)",
        "8.4 Local HBD probabilities",
        "8.5 HBD segments",
        "8.6 Accessor functions (easier access to slots)",
        "8.6.1 For realized autozygosity",
        "8.6.2 For inbreeding coefficients",
        "8.6.3 For inbreeding coefficients estimated from HBD segments",
        "8.6.4 For HBD segments",
        "8.6.5 For local HBD probabilities (locus specific)",
        "8.6.6 Using accessor functions with the IBD analysis",
        "8.6.7 Combining accessor functions with standard summary functions",
        "8.6.8 Merging and updating zres objects",
        "9 Plotting",
        "9.1. Proportion of the genome associated with different HBD classes (population)",
        "9.2. Proportion of the genome associated with different HBD classes (individuals)",
        "9.3. Partitioning individual genomes in different HBD classes",
        "9.4. Plotting identified HBD segments",
        "10 Impact of data quality and informativity - some caution with whole genome sequecing and reduced representation sequecing",
        "11 Predicting HBD in future offspring and kinship estimation with \\texttt",
        "11.1 Running the model",
        "11.2 Output",
        "11.3 Specific accessor function"
      ],
      "created": "2018-06-19 07:55:35",
      "modified": "2026-10-02 18:32:24",
      "commits": 8
    }
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