Pedigree Functions
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Documentation for package ‘Pedixplorer’ version 1.2.0
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A B C D F G H I K L M N P R S U misc
| Pedixplorer-package | The Pedixplorer package for pedigree data |
-- A --
| affected | Ped object |
| affected-method | Ped object |
| affected<- | Ped object |
| affected<--method | Ped object |
| align | Align a Pedigree object |
| align-method | Align a Pedigree object |
| alignped1 | Alignment first routine |
| alignped2 | Alignment second routine |
| alignped3 | Alignment third routine |
| alignped4 | Alignment fourth routine |
| as.data.frame-method | Ped object |
| as.data.frame-method | Rel object |
| as.list-method | Hints object |
| as.list-method | Ped object |
| as.list-method | Pedigree object |
| as.list-method | Rel object |
| as.list-method | Scales object |
| auto_hint | Initial hint for a Pedigree alignment |
| auto_hint-method | Initial hint for a Pedigree alignment |
| avail | Ped object |
| avail-method | Ped object |
| avail<- | Ped object |
| avail<--method | Ped object |
-- B --
| best_hint | Best hint for a Pedigree alignment |
| best_hint-method | Best hint for a Pedigree alignment |
| bit_size | Bit size of a Pedigree |
| bit_size-method | Bit size of a Pedigree |
| border | Scales object |
| border-method | Pedigree object |
| border-method | Scales object |
| border<- | Scales object |
| border<--method | Pedigree object |
| border<--method | Scales object |
-- C --
| code | Rel object |
| code-method | Rel object |
-- D --
| dadid | Ped object |
| dadid-method | Ped object |
| dadid<- | Ped object |
| dadid<--method | Ped object |
-- F --
| famid | Ped object |
| famid-method | Ped object |
| famid-method | Rel object |
| famid<- | Ped object |
| famid<--method | Ped object |
| famid<--method | Rel object |
| family_infos_table | Affection and availability information table |
| fill | Scales object |
| fill-method | Pedigree object |
| fill-method | Scales object |
| fill<- | Scales object |
| fill<--method | Pedigree object |
| fill<--method | Scales object |
| find_avail_affected | Find single affected and available individual from a Pedigree |
| find_avail_affected-method | Find single affected and available individual from a Pedigree |
| find_avail_noninform | Find uninformative but available subject |
| find_avail_noninform-method | Find uninformative but available subject |
| find_unavailable | Find unavailable subjects in a Pedigree |
| find_unavailable-method | Find unavailable subjects in a Pedigree |
| fix_parents | Fix parents relationship and gender |
| fix_parents-method | Fix parents relationship and gender |
-- G --
| generate_colors | Process the filling and border colors based on affection and availability |
| generate_colors-method | Process the filling and border colors based on affection and availability |
-- H --
| Hints | Hints object |
| hints | Pedigree object |
| Hints-class | Hints object |
| Hints-method | Hints object |
| hints-method | Pedigree object |
| hints<- | Pedigree object |
| hints<--method | Pedigree object |
| horder | Hints object |
| horder-method | Hints object |
| horder-method | Pedigree object |
| horder<- | Hints object |
| horder<--method | Hints object |
| horder<--method | Pedigree object |
-- I --
| ibd_matrix | IBD matrix |
| id | Ped object |
| id-method | Ped object |
| id1 | Rel object |
| id1-method | Rel object |
| id2 | Rel object |
| id2-method | Rel object |
| id<- | Ped object |
| id<--method | Ped object |
| isinf | Ped object |
| isinf-method | Ped object |
| isinf<- | Ped object |
| isinf<--method | Ped object |
| is_informative | Find informative individuals |
| is_informative-method | Find informative individuals |
| is_parent | Are individuals parents |
| is_parent-method | Are individuals parents |
-- K --
| kin | Ped object |
| kin-method | Ped object |
| kin<- | Ped object |
| kin<--method | Ped object |
| kindepth | Individual's depth in a pedigree |
| kindepth-method | Individual's depth in a pedigree |
| kinship | Kinship matrix |
| kinship-method | Kinship matrix |
-- L --
| length-method | Pedigree object |
-- M --
| make_famid | Compute family id |
| make_famid-method | Compute family id |
| mcols-method | Pedigree object |
| mcols<--method | Ped object |
| mcols<--method | Pedigree object |
| minnbreast | Minnesota Breast Cancer Study |
| min_dist_inf | Minimum distance to the informative individuals |
| min_dist_inf-method | Minimum distance to the informative individuals |
| momid | Ped object |
| momid-method | Ped object |
| momid<- | Ped object |
| momid<--method | Ped object |
-- N --
| norm_ped | Normalise a Ped object dataframe |
| norm_rel | Normalise a Rel object dataframe |
| num_child | Number of childs |
| num_child-method | Number of childs |
-- P --
| parent_of | Get parents of individuals |
| parent_of-method | Get parents of individuals |
| Ped | Ped object |
| ped | Pedigree object |
| Ped-class | Ped object |
| Ped-method | Ped object |
| ped-method | Pedigree object |
| ped<- | Pedigree object |
| ped<--method | Pedigree object |
| Pedigree | Pedigree object |
| Pedigree-class | Pedigree object |
| Pedigree-method | Pedigree object |
| Pedixplorer | The Pedixplorer package for pedigree data |
| ped_shiny | Run Pedixplorer Shiny application |
| ped_to_legdf | Create plotting legend data frame from a Pedigree |
| ped_to_legdf-method | Create plotting legend data frame from a Pedigree |
| ped_to_plotdf | Create plotting data frame from a Pedigree |
| ped_to_plotdf-method | Create plotting data frame from a Pedigree |
| plot,Pedigree | Plot Pedigrees |
| plot-method | Plot Pedigrees |
| plot.Pedigree | Plot Pedigrees |
| plot_fromdf | Create a plot from a data.frame |
-- R --
| Rel | Rel object |
| rel | Pedigree object |
| Rel-class | Rel object |
| Rel-method | Rel object |
| rel-method | Pedigree object |
| rel<- | Pedigree object |
| rel<--method | Pedigree object |
| relped | Relped data |
-- S --
| sampleped | Sampleped data |
| Scales | Scales object |
| scales | Pedigree object |
| Scales-class | Scales object |
| Scales-method | Scales object |
| scales-method | Pedigree object |
| scales<- | Pedigree object |
| scales<--method | Pedigree object |
| sex | Ped object |
| sex-method | Ped object |
| sex<- | Ped object |
| sex<--method | Ped object |
| show-method | Ped object |
| show-method | Pedigree object |
| show-method | Rel object |
| shrink | Shrink Pedigree object |
| shrink-method | Shrink Pedigree object |
| spouse | Hints object |
| spouse-method | Hints object |
| spouse-method | Pedigree object |
| spouse<- | Pedigree object |
| spouse<--method | Hints object |
| spouse<--method | Pedigree object |
| status | Ped object |
| status-method | Ped object |
| status<- | Ped object |
| status<--method | Ped object |
| subset-method | Hints object |
| subset-method | Ped object |
| subset-method | Pedigree object |
| subset-method | Rel object |
| summary-method | Ped object |
| summary-method | Pedigree object |
| summary-method | Rel object |
-- U --
| unrelated | Find Unrelated subjects |
| unrelated-method | Find Unrelated subjects |
| upd_famid | Update family prefix in individuals id |
| upd_famid-method | Update family prefix in individuals id |
| useful | Ped object |
| useful-method | Ped object |
| useful<- | Ped object |
| useful<--method | Ped object |
| useful_inds | Usefulness of individuals |
| useful_inds-method | Usefulness of individuals |
-- misc --
| [-method | Pedigree object |