Package: Pedixplorer 1.9.2
Louis Le Nezet
Pedixplorer: Pedigree Functions
Routines to handle family data with a Pedigree object. The initial purpose was to create correlation structures that describe family relationships such as kinship and identity-by-descent, which can be used to model family data in mixed effects models, such as in the coxme function. Also includes a tool for Pedigree drawing which is focused on producing compact layouts without intervention. Recent additions include utilities to trim the Pedigree object with various criteria, and kinship for the X chromosome.
Authors:
Pedixplorer_1.9.2.tar.gz
Pedixplorer_1.9.2.zip(r-4.7)Pedixplorer_1.9.2.zip(r-4.6)Pedixplorer_1.9.2.zip(r-4.5)
Pedixplorer_1.9.2.tgz(r-4.6-any)Pedixplorer_1.9.2.tgz(r-4.5-any)
Pedixplorer_1.9.2.tar.gz(r-4.7-any)Pedixplorer_1.9.2.tar.gz(r-4.6-any)
Pedixplorer_1.9.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
Pedixplorer/json (API)
NEWS
| # Install 'Pedixplorer' in R: |
| install.packages('Pedixplorer', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/louislenezet/pedixplorer/issues
Pkgdown/docs site:https://louislenezet.github.io
- minnbreast - Minnesota Breast Cancer Study
- relped - Relped data
- sampleped - Sampleped data
On BioConductor:Pedixplorer-1.9.0(bioc 3.24)Pedixplorer-1.8.0(bioc 3.23)
softwaredatarepresentationgeneticsgraphandnetworkvisualizationkinshippedigree
Last updated from:a114955946. Checks:1 NOTE, 7 WARNING, 1 ERROR, 1 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 220 | ||
| linux-devel-x86_64 | WARNING | 333 | ||
| source / vignettes | ERROR | 298 | ||
| linux-release-x86_64 | WARNING | 349 | ||
| macos-release-arm64 | WARNING | 205 | ||
| macos-oldrel-arm64 | WARNING | 176 | ||
| windows-devel | WARNING | 276 | ||
| windows-release | WARNING | 264 | ||
| windows-oldrel | WARNING | 256 | ||
| wasm-release | OK | 153 |
Exports:adoptedadopted<-affectedaffected<-alignancestorsas.data.frameas.listasymptomaticasymptomatic<-auto_hintavailavail<-best_hintbit_sizeborderborder<-carriercarrier<-codecolor_picker_democolor_picker_servercompute_stressconsultandconsultand<-dadiddadid<-data_col_sel_demodata_download_demodata_import_demodateofbirthdateofbirth<-dateofdeathdateofdeath<-deceaseddeceased<-descendantseval_permevaluatedevaluated<-famidfamid<-family_checkfamily_sel_demofertilityfertility_to_factorfertility<-fillfill<-find_avail_affectedfind_avail_noninformfind_unavailablefix_parentsgenerate_aff_indsgenerate_bordergenerate_colorsgenerate_fillget_famidget_families_tableget_titlehealth_sel_demohintsHintshints<-horderhorder<-ibd_matrixidid<-id1id2inf_sel_demois_disconnectedis_founderis_informativeis_parentisinfisinf<-kinkin<-kindepthkinshipmake_famidmake_reactivemcolsmcols<-min_dist_infmiscarriagemiscarriage_to_factormiscarriage<-momidmomid<-norm_pednorm_relnum_childparent_ofpedPedped_avaf_infos_demoped_serverped_shinyped_to_legdfped_to_plotdfped_uiped<-Pedigreeplink_to_pedigreeplotplot_download_demoplot_fromdfplot_legend_demoplot_legend_serverplot_legend_uiplot_ped_demoplot_resize_serverprobandproband<-relRelrel_code_to_factorrel<-rescalescalesScalesscales<-sexsex_to_factorsex<-showshrinkspousespouse<-subsetsummaryunrelatedupd_famidusefuluseful_indsuseful<-vect_to_binary
Dependencies:askpassbase64encBiocGenericsbslibcachemcellrangerclicolourpickercommonmarkcpp11crayoncrosstalkcurldata.tabledigestdplyrDTevaluatefarverfastmapfontawesomefsgenericsggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttpuvhttrigraphisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelitedownmagrittrmarkdownMatrixmemoisemimeminiUIopensslotelpillarpkgconfigplotlyplyrprettyunitsprogresspromisespurrrquadprogR6rappdirsRColorBrewerRcppreadxlrematchrlangrmarkdownS4VectorsS7sassscalesshinyshinycssloadersshinyhelpershinyjquishinyjsshinytoastrshinyWidgetssourcetoolsstringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunxtableyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| The Pedixplorer package for pedigree data | Pedixplorer-package Pedixplorer |
| Align a Pedigree object | align align,Pedigree-method |
| Alignment first routine | alignped1 |
| Alignment second routine | alignped2 |
| Alignment third routine | alignped3 |
| Alignment fourth routine | alignped4 |
| Initial hint for a Pedigree alignment | auto_hint auto_hint,Pedigree-method |
| Best hint for a Pedigree alignment | best_hint best_hint,Pedigree-method |
| Bit size of a Pedigree | bit_size bit_size,character_OR_integer-method bit_size,Ped-method bit_size,Pedigree-method |
| Affection and availability information table | family_infos_table |
| Find single affected and available individual from a Pedigree | find_avail_affected find_avail_affected,Ped-method find_avail_affected,Pedigree-method |
| Find uninformative but available subject | find_avail_noninform find_avail_noninform,Ped-method find_avail_noninform,Pedigree-method |
| Find unavailable subjects in a Pedigree | find_unavailable find_unavailable,Ped-method find_unavailable,Pedigree-method |
| Fix parents relationship and gender | fix_parents fix_parents,character-method fix_parents,data.frame-method |
| Process the filling and border colors based on affection and availability | generate_colors generate_colors,character-method generate_colors,numeric-method generate_colors,Pedigree-method |
| Hints object | 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 |
| IBD matrix | ibd_matrix |
| Find informative individuals | is_informative is_informative,character_OR_integer-method is_informative,Ped-method is_informative,Pedigree-method |
| Are individuals parents | is_parent is_parent,character_OR_integer-method is_parent,Ped-method |
| Individual's depth in a pedigree | kindepth kindepth,character_OR_integer-method kindepth,Ped-method kindepth,Pedigree-method |
| Kinship matrix | kinship kinship,character-method kinship,Ped-method kinship,Pedigree-method |
| Compute family id | make_famid make_famid,character-method make_famid,Pedigree-method |
| Minimum distance to the informative individuals | min_dist_inf min_dist_inf,character-method min_dist_inf,Ped-method min_dist_inf,Pedigree-method |
| Minnesota Breast Cancer Study | minnbreast |
| Normalise a Ped object dataframe | norm_ped |
| Normalise a Rel object dataframe | norm_rel |
| Number of childs | num_child num_child,character_OR_integer-method num_child,Pedigree-method |
| Get parents of individuals | parent_of parent_of,character_OR_integer-method parent_of,Ped-method parent_of,Pedigree-method |
| Create the server logic for the ped_shiny application | ped_server |
| Run Pedixplorer Shiny application | ped_shiny |
| Create plotting legend data frame from a Pedigree | ped_to_legdf ped_to_legdf,Pedigree-method |
| Create plotting data frame from a Pedigree | ped_to_plotdf ped_to_plotdf,Pedigree-method |
| Create the user interface for the ped_shiny application | ped_ui |
| Ped object | 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 |
| Pedigree object | 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 |
| Import from .fam file or .ped file | plink_to_pedigree |
| Create a plot from a data.frame | plot_fromdf |
| Plot Pedigrees | plot,Pedigree plot,Pedigree,missing-method plot.Pedigree |
| Rel object | 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 |
| Relped data | relped |
| Sampleped data | sampleped |
| Scales object | 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 |
| Shrink Pedigree object | shrink shrink,Ped-method shrink,Pedigree-method |
| Find Unrelated subjects | unrelated unrelated,Ped-method unrelated,Pedigree-method |
| Update family prefix in individuals id | 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 |
| Usefulness of individuals | useful_inds useful_inds,character-method useful_inds,Ped-method useful_inds,Pedigree-method |
