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"momid", "sex", "affection", "avail", "num", "fertility", "miscarriage", "evaluated", "consultand", "proband", "carrier", "asymptomatic", "adopted", "dateofbirth", "dateofdeath", "deceased" ], "rows": 55, "table": true, "tojson": true } ], "_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", 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