{
  "_id": "6a1ac00e1d7bb097a09d683d",
  "Package": "Pedixplorer",
  "Version": "1.9.0",
  "Date": "2025-08-26",
  "Title": "Pedigree Functions",
  "Authors@R": "c(\nperson(\"Louis\", \"Le Nezet\", email=\"louislenezet@gmail.com\",\nrole=c(\"aut\",\"cre\",\"ctb\"), comment = c(ORCID = \"0009-0000-0202-2703\")),\nperson(\"Jason\", \"Sinnwell\", email=\"sinnwell.jason@mayo.edu\", role=\"aut\"),\nperson(\"Terry\", \"Therneau\", role=\"aut\"),\nperson(\"Daniel\", \"Schaid\", role=\"ctb\"),\nperson(\"Elizabeth\", \"Atkinson\", role=\"ctb\"))",
  "Description": "Routines to handle family data with a Pedigree object. The\ninitial purpose was to create correlation structures that\ndescribe family relationships such as kinship and\nidentity-by-descent, which can be used to model family data in\nmixed effects models, such as in the coxme function. Also\nincludes a tool for Pedigree drawing which is focused on\nproducing compact layouts without intervention. Recent\nadditions include utilities to trim the Pedigree object with\nvarious criteria, and kinship for the X chromosome.",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.3",
  "Roxygen": "list(markdown = TRUE)",
  "VignetteBuilder": "knitr",
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  "biocViews": "Software, DataRepresentation, Genetics, GraphAndNetwork,\nVisualization",
  "BugReports": "https://github.com/LouisLeNezet/Pedixplorer/issues",
  "URL": "https://louislenezet.github.io/Pedixplorer/",
  "BiocType": "Software",
  "Collate": "'AllValidity.R' 'AllClass.R' 'kindepth.R' 'kinship.R'\n'utils.R' 'AllConstructor.R' 'AllAccessors.R' 'AllGeneric.R'\n'Pedixplorer-package.R' 'alignped4.R' 'alignped3.R'\n'alignped2.R' 'alignped1.R' 'auto_hint.R' 'align.R' 'app.R'\n'app_color_picker.R' 'app_data_col_sel.R' 'app_data_download.R'\n'app_data_import.R' 'app_utils.R' 'app_family_sel.R'\n'app_health_sel.R' 'app_inf_sel.R' 'app_ped_avaf_infos.R'\n'app_plot_resize.R' 'app_plot_download.R' 'app_plot_legend.R'\n'app_plot_ped.R' 'app_plot_all.R' 'app_server.R' 'app_ui.R'\n'best_hint.R' 'bit_size.R' 'data.R' 'descendants.R'\n'family_check.R' 'find_unavailable.R' 'find_avail_affected.R'\n'find_avail_noninform.R' 'fix_parents.R' 'generate_aff_inds.R'\n'generate_colors.R' 'ibd_matrix.R' 'is_informative.R'\n'make_famid.R' 'min_dist_inf.R' 'norm_data.R' 'num_child.R'\n'ped_to_legdf.R' 'ped_to_plotdf.R' 'plot_fct.R' 'plot_fromdf.R'\n'plot_pedigree.R' 'shrink.R' 'unrelated.R' 'useful_inds.R'",
  "LazyData": "false",
  "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:02:23 UTC",
  "RemoteUrl": "https://github.com/bioc/Pedixplorer",
  "RemoteRef": "HEAD",
  "RemoteSha": "8e9806c45e6d236f454f3429838a45e85ca4eb08",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 07:14:26 UTC",
    "User": "root"
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  "Author": "Louis Le Nezet [aut, cre, ctb] (ORCID:\n<https://orcid.org/0009-0000-0202-2703>),\nJason Sinnwell [aut],\nTerry Therneau [aut],\nDaniel Schaid [ctb],\nElizabeth Atkinson [ctb]",
  "Maintainer": "Louis Le Nezet <louislenezet@gmail.com>",
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  "_created": "2026-05-30T07:14:26.000Z",
  "_published": "2026-05-30T10:46:38.246Z",
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    "adopted<-",
    "affected",
    "affected<-",
    "align",
    "ancestors",
    "as.data.frame",
    "as.list",
    "asymptomatic",
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    "auto_hint",
    "avail",
    "avail<-",
    "best_hint",
    "bit_size",
    "border",
    "border<-",
    "carrier",
    "carrier<-",
    "code",
    "color_picker_demo",
    "color_picker_server",
    "compute_stress",
    "consultand",
    "consultand<-",
    "dadid",
    "dadid<-",
    "data_col_sel_demo",
    "data_download_demo",
    "data_import_demo",
    "dateofbirth",
    "dateofbirth<-",
    "dateofdeath",
    "dateofdeath<-",
    "deceased",
    "deceased<-",
    "descendants",
    "eval_perm",
    "evaluated",
    "evaluated<-",
    "famid",
    "famid<-",
    "family_check",
    "family_sel_demo",
    "fertility",
    "fertility_to_factor",
    "fertility<-",
    "fill",
    "fill<-",
    "find_avail_affected",
    "find_avail_noninform",
    "find_unavailable",
    "fix_parents",
    "generate_aff_inds",
    "generate_border",
    "generate_colors",
    "generate_fill",
    "get_famid",
    "get_families_table",
    "get_title",
    "health_sel_demo",
    "hints",
    "Hints",
    "hints<-",
    "horder",
    "horder<-",
    "ibd_matrix",
    "id",
    "id<-",
    "id1",
    "id2",
    "inf_sel_demo",
    "is_disconnected",
    "is_founder",
    "is_informative",
    "is_parent",
    "isinf",
    "isinf<-",
    "kin",
    "kin<-",
    "kindepth",
    "kinship",
    "make_famid",
    "make_reactive",
    "mcols",
    "mcols<-",
    "min_dist_inf",
    "miscarriage",
    "miscarriage_to_factor",
    "miscarriage<-",
    "momid",
    "momid<-",
    "norm_ped",
    "norm_rel",
    "num_child",
    "parent_of",
    "ped",
    "Ped",
    "ped_avaf_infos_demo",
    "ped_server",
    "ped_shiny",
    "ped_to_legdf",
    "ped_to_plotdf",
    "ped_ui",
    "ped<-",
    "Pedigree",
    "plink_to_pedigree",
    "plot",
    "plot_download_demo",
    "plot_fromdf",
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    "plot_legend_server",
    "plot_legend_ui",
    "plot_ped_demo",
    "plot_resize_server",
    "proband",
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    "Rel",
    "rel_code_to_factor",
    "rel<-",
    "rescale",
    "scales",
    "Scales",
    "scales<-",
    "sex",
    "sex_to_factor",
    "sex<-",
    "show",
    "shrink",
    "spouse",
    "spouse<-",
    "subset",
    "summary",
    "unrelated",
    "upd_famid",
    "useful",
    "useful_inds",
    "useful<-",
    "vect_to_binary"
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      "title": "Minnesota Breast Cancer Study",
      "object": "minnbreast",
      "file": "minnbreast.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
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        "proband",
        "fatherid",
        "motherid",
        "famid",
        "endage",
        "cancer",
        "yob",
        "education",
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        "everpreg",
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        "nbreast",
        "sex",
        "bcpc"
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      "table": true,
      "tojson": true
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      "class": [
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        "id1",
        "id2",
        "code"
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      "title": "Sampleped data",
      "object": "sampleped",
      "file": "sampleped.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
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        "id",
        "dadid",
        "momid",
        "sex",
        "affection",
        "avail",
        "num",
        "fertility",
        "miscarriage",
        "evaluated",
        "consultand",
        "proband",
        "carrier",
        "asymptomatic",
        "adopted",
        "dateofbirth",
        "dateofdeath",
        "deceased"
      ],
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      "table": true,
      "tojson": true
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  "_help": [
    {
      "page": "Pedixplorer_package",
      "title": "The Pedixplorer package for pedigree data",
      "topics": [
        "Pedixplorer-package",
        "Pedixplorer"
      ]
    },
    {
      "page": "align",
      "title": "Align a Pedigree object",
      "topics": [
        "align",
        "align,Pedigree-method"
      ]
    },
    {
      "page": "alignped1",
      "title": "Alignment first routine",
      "topics": [
        "alignped1"
      ]
    },
    {
      "page": "alignped2",
      "title": "Alignment second routine",
      "topics": [
        "alignped2"
      ]
    },
    {
      "page": "alignped3",
      "title": "Alignment third routine",
      "topics": [
        "alignped3"
      ]
    },
    {
      "page": "alignped4",
      "title": "Alignment fourth routine",
      "topics": [
        "alignped4"
      ]
    },
    {
      "page": "auto_hint",
      "title": "Initial hint for a Pedigree alignment",
      "topics": [
        "auto_hint",
        "auto_hint,Pedigree-method"
      ]
    },
    {
      "page": "best_hint",
      "title": "Best hint for a Pedigree alignment",
      "topics": [
        "best_hint",
        "best_hint,Pedigree-method"
      ]
    },
    {
      "page": "bit_size",
      "title": "Bit size of a Pedigree",
      "topics": [
        "bit_size",
        "bit_size,character_OR_integer-method",
        "bit_size,Ped-method",
        "bit_size,Pedigree-method"
      ]
    },
    {
      "page": "family_infos_table",
      "title": "Affection and availability information table",
      "topics": [
        "family_infos_table"
      ]
    },
    {
      "page": "find_avail_affected",
      "title": "Find single affected and available individual from a Pedigree",
      "topics": [
        "find_avail_affected",
        "find_avail_affected,Ped-method",
        "find_avail_affected,Pedigree-method"
      ]
    },
    {
      "page": "find_avail_noninform",
      "title": "Find uninformative but available subject",
      "topics": [
        "find_avail_noninform",
        "find_avail_noninform,Ped-method",
        "find_avail_noninform,Pedigree-method"
      ]
    },
    {
      "page": "find_unavailable",
      "title": "Find unavailable subjects in a Pedigree",
      "topics": [
        "find_unavailable",
        "find_unavailable,Ped-method",
        "find_unavailable,Pedigree-method"
      ]
    },
    {
      "page": "fix_parents",
      "title": "Fix parents relationship and gender",
      "topics": [
        "fix_parents",
        "fix_parents,character-method",
        "fix_parents,data.frame-method"
      ]
    },
    {
      "page": "generate_colors",
      "title": "Process the filling and border colors based on affection and availability",
      "topics": [
        "generate_colors",
        "generate_colors,character-method",
        "generate_colors,numeric-method",
        "generate_colors,Pedigree-method"
      ]
    },
    {
      "page": "Hints-class",
      "title": "Hints object",
      "topics": [
        "as.list,Hints-method",
        "Hints",
        "Hints,Hints,missing_OR_NULL-method",
        "Hints,list,missing_OR_NULL-method",
        "Hints,missing_OR_NULL,data.frame-method",
        "Hints,missing_OR_NULL,missing_OR_NULL-method",
        "Hints,numeric,data.frame-method",
        "Hints,numeric,missing_OR_NULL-method",
        "Hints-class",
        "horder",
        "horder,Hints-method",
        "horder<-",
        "horder<-,Hints-method",
        "spouse",
        "spouse,Hints-method",
        "spouse<-,Hints,data.frame-method",
        "subset,Hints-method"
      ]
    },
    {
      "page": "ibd_matrix",
      "title": "IBD matrix",
      "topics": [
        "ibd_matrix"
      ]
    },
    {
      "page": "is_informative",
      "title": "Find informative individuals",
      "topics": [
        "is_informative",
        "is_informative,character_OR_integer-method",
        "is_informative,Ped-method",
        "is_informative,Pedigree-method"
      ]
    },
    {
      "page": "is_parent",
      "title": "Are individuals parents",
      "topics": [
        "is_parent",
        "is_parent,character_OR_integer-method",
        "is_parent,Ped-method"
      ]
    },
    {
      "page": "kindepth",
      "title": "Individual's depth in a pedigree",
      "topics": [
        "kindepth",
        "kindepth,character_OR_integer-method",
        "kindepth,Ped-method",
        "kindepth,Pedigree-method"
      ]
    },
    {
      "page": "kinship",
      "title": "Kinship matrix",
      "topics": [
        "kinship",
        "kinship,character-method",
        "kinship,Ped-method",
        "kinship,Pedigree-method"
      ]
    },
    {
      "page": "make_famid",
      "title": "Compute family id",
      "topics": [
        "make_famid",
        "make_famid,character-method",
        "make_famid,Pedigree-method"
      ]
    },
    {
      "page": "min_dist_inf",
      "title": "Minimum distance to the informative individuals",
      "topics": [
        "min_dist_inf",
        "min_dist_inf,character-method",
        "min_dist_inf,Ped-method",
        "min_dist_inf,Pedigree-method"
      ]
    },
    {
      "page": "minnbreast",
      "title": "Minnesota Breast Cancer Study",
      "topics": [
        "minnbreast"
      ]
    },
    {
      "page": "norm_ped",
      "title": "Normalise a Ped object dataframe",
      "topics": [
        "norm_ped"
      ]
    },
    {
      "page": "norm_rel",
      "title": "Normalise a Rel object dataframe",
      "topics": [
        "norm_rel"
      ]
    },
    {
      "page": "num_child",
      "title": "Number of childs",
      "topics": [
        "num_child",
        "num_child,character_OR_integer-method",
        "num_child,Pedigree-method"
      ]
    },
    {
      "page": "parent_of",
      "title": "Get parents of individuals",
      "topics": [
        "parent_of",
        "parent_of,character_OR_integer-method",
        "parent_of,Ped-method",
        "parent_of,Pedigree-method"
      ]
    },
    {
      "page": "ped_server",
      "title": "Create the server logic for the ped_shiny application",
      "topics": [
        "ped_server"
      ]
    },
    {
      "page": "ped_shiny",
      "title": "Run Pedixplorer Shiny application",
      "topics": [
        "ped_shiny"
      ]
    },
    {
      "page": "ped_to_legdf",
      "title": "Create plotting legend data frame from a Pedigree",
      "topics": [
        "ped_to_legdf",
        "ped_to_legdf,Pedigree-method"
      ]
    },
    {
      "page": "ped_to_plotdf",
      "title": "Create plotting data frame from a Pedigree",
      "topics": [
        "ped_to_plotdf",
        "ped_to_plotdf,Pedigree-method"
      ]
    },
    {
      "page": "ped_ui",
      "title": "Create the user interface for the ped_shiny application",
      "topics": [
        "ped_ui"
      ]
    },
    {
      "page": "Ped-class",
      "title": "Ped object",
      "topics": [
        "adopted",
        "adopted,Ped-method",
        "adopted<-",
        "adopted<-,Ped,numeric_OR_logical-method",
        "affected",
        "affected,Ped-method",
        "affected<-",
        "affected<-,Ped,numeric_OR_logical-method",
        "as.data.frame,Ped-method",
        "as.list,Ped-method",
        "asymptomatic",
        "asymptomatic,Ped-method",
        "asymptomatic<-",
        "asymptomatic<-,Ped,numeric_OR_logical-method",
        "avail",
        "avail,Ped-method",
        "avail<-",
        "avail<-,Ped,numeric_OR_logical-method",
        "carrier",
        "carrier,Ped-method",
        "carrier<-",
        "carrier<-,Ped,numeric_OR_logical-method",
        "consultand",
        "consultand,Ped-method",
        "consultand<-",
        "consultand<-,Ped,numeric_OR_logical-method",
        "dadid",
        "dadid,Ped-method",
        "dadid<-",
        "dadid<-,Ped,character_OR_integer-method",
        "dateofbirth",
        "dateofbirth,Ped-method",
        "dateofbirth<-",
        "dateofbirth<-,Ped,Date_OR_character-method",
        "dateofdeath",
        "dateofdeath,Ped-method",
        "dateofdeath<-",
        "dateofdeath<-,Ped,Date_OR_character-method",
        "deceased",
        "deceased,Ped-method",
        "deceased<-",
        "deceased<-,Ped,numeric_OR_logical-method",
        "evaluated",
        "evaluated,Ped-method",
        "evaluated<-",
        "evaluated<-,Ped,numeric_OR_logical-method",
        "famid",
        "famid,Ped-method",
        "famid<-",
        "famid<-,Ped,character_OR_integer-method",
        "fertility",
        "fertility,Ped-method",
        "fertility<-",
        "fertility<-,Ped,character_OR_integer-method",
        "id",
        "id,Ped-method",
        "id<-",
        "id<-,Ped,character_OR_integer-method",
        "isinf",
        "isinf,Ped-method",
        "isinf<-",
        "isinf<-,Ped,numeric_OR_logical-method",
        "kin",
        "kin,Ped-method",
        "kin<-",
        "kin<-,Ped,numeric-method",
        "mcols<-,Ped,data.frame-method",
        "mcols<-,Ped,list-method",
        "miscarriage",
        "miscarriage,Ped-method",
        "miscarriage<-",
        "miscarriage<-,Ped,character_OR_integer-method",
        "momid",
        "momid,Ped-method",
        "momid<-",
        "momid<-,Ped,character_OR_integer-method",
        "Ped",
        "Ped,character_OR_integer-method",
        "Ped,data.frame-method",
        "Ped,missing-method",
        "Ped-class",
        "proband",
        "proband,Ped-method",
        "proband<-",
        "proband<-,Ped,numeric_OR_logical-method",
        "sex",
        "sex,Ped-method",
        "sex<-",
        "sex<-,Ped,character_OR_integer-method",
        "show,Ped-method",
        "subset,Ped-method",
        "summary,Ped-method",
        "useful",
        "useful,Ped-method",
        "useful<-",
        "useful<-,Ped,numeric_OR_logical-method"
      ]
    },
    {
      "page": "Pedigree-class",
      "title": "Pedigree object",
      "topics": [
        "as.list,Pedigree-method",
        "border,Pedigree-method",
        "border<-,Pedigree,data.frame-method",
        "fill,Pedigree-method",
        "fill<-,Pedigree,data.frame-method",
        "hints",
        "hints,Pedigree-method",
        "hints<-",
        "hints<-,Pedigree,Hints-method",
        "horder,Pedigree-method",
        "horder<-,Pedigree-method",
        "length,Pedigree-method",
        "mcols,Pedigree-method",
        "mcols<-,Pedigree,ANY-method",
        "ped",
        "ped,Pedigree,ANY-method",
        "ped,Pedigree,missing-method",
        "ped<-",
        "ped<-,Pedigree,ANY,ANY-method",
        "ped<-,Pedigree,missing,Ped-method",
        "Pedigree",
        "Pedigree,character_OR_integer-method",
        "Pedigree,data.frame-method",
        "Pedigree,missing-method",
        "Pedigree-class",
        "rel",
        "rel,Pedigree,ANY-method",
        "rel,Pedigree,missing-method",
        "rel<-",
        "rel<-,Pedigree,ANY,ANY-method",
        "rel<-,Pedigree,missing,Rel-method",
        "scales",
        "scales,Pedigree-method",
        "scales<-",
        "scales<-,Pedigree,Scales-method",
        "show,Pedigree-method",
        "spouse,Pedigree-method",
        "spouse<-",
        "spouse<-,Pedigree,data.frame-method",
        "subset,Pedigree-method",
        "summary,Pedigree-method",
        "[,Pedigree,ANY,missing,ANY-method"
      ]
    },
    {
      "page": "plink_to_pedigree",
      "title": "Import from .fam file or .ped file",
      "topics": [
        "plink_to_pedigree"
      ]
    },
    {
      "page": "plot_fromdf",
      "title": "Create a plot from a data.frame",
      "topics": [
        "plot_fromdf"
      ]
    },
    {
      "page": "plot_pedigree",
      "title": "Plot Pedigrees",
      "topics": [
        "plot,Pedigree",
        "plot,Pedigree,missing-method",
        "plot.Pedigree"
      ]
    },
    {
      "page": "Rel-class",
      "title": "Rel object",
      "topics": [
        "as.data.frame,Rel-method",
        "as.list,Rel-method",
        "code",
        "code,Rel-method",
        "famid,Rel-method",
        "famid<-,Rel,character_OR_integer-method",
        "id1",
        "id1,Rel-method",
        "id2",
        "id2,Rel-method",
        "Rel",
        "Rel,character_OR_integer-method",
        "Rel,data.frame-method",
        "Rel,missing-method",
        "Rel-class",
        "show,Rel-method",
        "subset,Rel-method",
        "summary,Rel-method"
      ]
    },
    {
      "page": "relped",
      "title": "Relped data",
      "topics": [
        "relped"
      ]
    },
    {
      "page": "sampleped",
      "title": "Sampleped data",
      "topics": [
        "sampleped"
      ]
    },
    {
      "page": "Scales-class",
      "title": "Scales object",
      "topics": [
        "as.list,Scales-method",
        "border",
        "border,Scales-method",
        "border<-",
        "border<-,Scales,data.frame-method",
        "fill",
        "fill,Scales-method",
        "fill<-",
        "fill<-,Scales,data.frame-method",
        "Scales",
        "Scales,data.frame,data.frame-method",
        "Scales,missing,missing-method",
        "Scales-class"
      ]
    },
    {
      "page": "shrink",
      "title": "Shrink Pedigree object",
      "topics": [
        "shrink",
        "shrink,Ped-method",
        "shrink,Pedigree-method"
      ]
    },
    {
      "page": "unrelated",
      "title": "Find Unrelated subjects",
      "topics": [
        "unrelated",
        "unrelated,Ped-method",
        "unrelated,Pedigree-method"
      ]
    },
    {
      "page": "upd_famid",
      "title": "Update family prefix in individuals id",
      "topics": [
        "upd_famid",
        "upd_famid,character,ANY-method",
        "upd_famid,Ped,character_OR_integer-method",
        "upd_famid,Ped,missing-method",
        "upd_famid,Pedigree,character_OR_integer-method",
        "upd_famid,Pedigree,missing-method",
        "upd_famid,Rel,character_OR_integer-method",
        "upd_famid,Rel,missing-method"
      ]
    },
    {
      "page": "useful_inds",
      "title": "Usefulness of individuals",
      "topics": [
        "useful_inds",
        "useful_inds,character-method",
        "useful_inds,Ped-method",
        "useful_inds,Pedigree-method"
      ]
    }
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  "_score": 5.547528576459783,
  "_indexed": true,
  "_nocasepkg": "pedixplorer",
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