Package: FamAgg 1.35.0

Johannes Rainer

FamAgg: Pedigree Analysis and Familial Aggregation

Framework providing basic pedigree analysis and plotting utilities as well as a variety of methods to evaluate familial aggregation of traits in large pedigrees.

Authors:J. Rainer, D. Taliun, C.X. Weichenberger

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FamAgg.pdf |FamAgg.html✨
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NEWS

# Install 'FamAgg' in R:

install.packages('FamAgg', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/euracbiomedicalresearch/famagg/issues

On BioConductor:FamAgg-1.35.0(bioc 3.21)FamAgg-1.34.0(bioc 3.20)

genetics pedigree

5.26 score 1 stars 5 scripts 206 downloads 3 mentions 64 exports 85 dependencies

Last updated 2 months agofrom:898172e9ce. Checks:OK: 3 NOTE: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win	NOTE	Nov 29 2024
R-4.5-linux	NOTE	Nov 29 2024
R-4.4-win	NOTE	Nov 29 2024
R-4.4-mac	NOTE	Nov 29 2024
R-4.3-win	OK	Nov 29 2024
R-4.3-mac	OK	Nov 29 2024

Exports:affectedIndividuals affectedKinshipGroups age age<-binomialTest buildPed cliqueAndTrait cliques cliques<-connectedSubgraph countGenerations doPlotPed estimateGenerations estimateTimeAtRisk export factor2matrix FAData familialIncidenceRate familialIncidenceRateTest family findFounders fsir fsirTest genealogicalIndexTest generationsFrom getAll getAncestors getChildren getCommonAncestor getExternalMatched getFounders getGenerationMatched getGenerationSexMatched getMissingMate getSexMatched getSiblings getSingletons kinship kinshipGroupTest kinshipPairs kinshipSumTest lambda ped2graph pedigree pedigree<-pedigreeSize phenotypedIndividuals plotPed plotRes probabilityTest removeSingletons result resultForId runSimulation shareKinship sliceAge subPedigree switchPlotfun timeAtRisk timeAtRisk<-timeInStrata trait trait<-traitByClique

Dependencies:askpass base64enc BiocGenerics bslib cachem cli colorspace cpp11 crosstalk curl data.table DBI digest dplyr evaluate fansi farver fastmap fontawesome fs gap gap.datasets generics ggplot2 glue gtable highr htmltools htmlwidgets httr igraph isoband jquerylib jsonlite kinship2 knitr labeling later lattice lazyeval lifecycle magrittr MASS Matrix memoise mgcv mime minqa mitools munsell nlme numDeriv openssl pillar pkgconfig plotly promises purrr quadprog R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo Rdpack rlang rmarkdown sass scales stringi stringr survey survival sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun yaml

Pedigree Analysis and Familial Aggregation

Rendered fromFamAgg.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2021-05-25
Started: 2015-11-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Binomial test for familial aggregation	FABinTestResults FABinTestResults-class result,FABinTestResults-method trait<-,FABinTestResults-method [,FABinTestResults,ANY,ANY,ANY-method [,FABinTestResults,ANY-method
Pedigree data information	$ $,FAData-method affectedIndividuals affectedIndividuals,FAData-method age age,FAData-method age<- age<-,FAData-method buildPed buildPed,FAData-method export export,FAData-method FAData FAData-class family family,FAData-method kinship kinship,FAData-method pedigree pedigree,FAData-method pedigree,missing-method pedigree<- pedigree<-,FAData-method pedigreeSize pedigreeSize,FAData-method phenotypedIndividuals phenotypedIndividuals,FAData-method plotPed plotPed,FAData-method show show,FAData-method trait trait,FAData-method trait<- trait<-,FAData-method [,FAData,ANY,ANY,ANY-method [,FAData,ANY-method
Genealogical Index	FAGenIndexResults FAGenIndexResults-class plotPed,FAGenIndexResults-method plotRes plotRes,FAGenIndexResults-method result,FAGenIndexResults-method runSimulation,FAGenIndexResults-method trait<-,FAGenIndexResults-method [,FAGenIndexResults,ANY,ANY,ANY-method [,FAGenIndexResults,ANY-method
Familial Incidence Rate	$,FAIncidenceRateResults-method FAIncidenceRateResults FAIncidenceRateResults-class familialIncidenceRate,FAIncidenceRateResults-method plotPed,FAIncidenceRateResults-method plotRes,FAIncidenceRateResults-method result,FAIncidenceRateResults-method runSimulation,FAIncidenceRateResults-method timeAtRisk timeAtRisk,FAIncidenceRateResults-method timeAtRisk<- timeAtRisk<-,FAIncidenceRateResults-method trait<-,FAIncidenceRateResults-method [,FAIncidenceRateResults,ANY,ANY,ANY-method [,FAIncidenceRateResults,ANY-method
Kinship group test	affectedKinshipGroups affectedKinshipGroups,FAKinGroupResults-method buildPed,FAKinGroupResults-method FAKinGroupResults FAKinGroupResults-class plotPed,FAKinGroupResults-method plotRes,FAKinGroupResults-method result,FAKinGroupResults-method runSimulation,FAKinGroupResults-method shareKinship,FAKinGroupResults-method trait<-,FAKinGroupResults-method [,FAKinGroupResults,ANY,ANY,ANY-method [,FAKinGroupResults,ANY-method
Kinship sum test	FAKinSumResults FAKinSumResults-class plotPed,FAKinSumResults-method plotRes,FAKinSumResults-method result,FAKinSumResults-method runSimulation,FAKinSumResults-method trait<-,FAKinSumResults-method [,FAKinSumResults,ANY,ANY,ANY-method [,FAKinSumResults,ANY-method
DEPRECATED: Probability test	buildPed,FAProbResults-method cliqueAndTrait cliqueAndTrait,FAProbResults-method cliques cliques,FAProbResults-method cliques<- cliques<-,FAProbResults-method FAProbResults FAProbResults-class plotPed,FAProbResults-method result result,FAProbResults-method runSimulation runSimulation,FAProbResults-method shareKinship,FAProbResults-method trait<-,FAProbResults-method traitByClique traitByClique,FAProbResults-method [,FAProbResults,ANY,ANY,ANY-method [,FAProbResults,ANY-method
Familial Standardized Incidence Rate	$,FAStdIncidenceRateResults-method FAStdIncidenceRateResults FAStdIncidenceRateResults-class fsir,FAStdIncidenceRateResults-method lambda lambda,FAStdIncidenceRateResults-method plotPed,FAStdIncidenceRateResults-method plotRes,FAStdIncidenceRateResults-method result,FAStdIncidenceRateResults-method resultForId resultForId,FAStdIncidenceRateResults-method runSimulation,FAStdIncidenceRateResults-method timeInStrata timeInStrata,FAStdIncidenceRateResults-method trait<-,FAStdIncidenceRateResults-method [,FAStdIncidenceRateResults,ANY,ANY,ANY-method [,FAStdIncidenceRateResults,ANY-method
Define sets of control individuals for one or more given individuals	getAll getAll,data.frame-method getAll,FAData-method getAll,pedigree-method getAll,pedigreeList-method getExternalMatched getExternalMatched,data.frame-method getExternalMatched,FAData-method getExternalMatched,pedigree-method getExternalMatched,pedigreeList-method getGenerationMatched getGenerationMatched,data.frame-method getGenerationMatched,FAData-method getGenerationMatched,pedigree-method getGenerationMatched,pedigreeList-method getGenerationSexMatched getGenerationSexMatched,data.frame-method getGenerationSexMatched,FAData-method getGenerationSexMatched,pedigree-method getGenerationSexMatched,pedigreeList-method getSexMatched getSexMatched,data.frame-method getSexMatched,FAData-method getSexMatched,pedigree-method getSexMatched,pedigreeList-method
Extract pairs of individuals matching certain kinship criteria	kinshipPairs
Pedigree analysis and familial aggregation methods	binomialTest estimateTimeAtRisk factor2matrix familialIncidenceRate familialIncidenceRate,FAData-method familialIncidenceRateTest familialIncidenceRateTest,FAData-method fsir fsir,FAData-method fsirTest fsirTest,FAData-method genealogicalIndexTest genealogicalIndexTest,FAData-method kinshipGroupTest kinshipGroupTest,FAData-method kinshipSumTest kinshipSumTest,FAData-method PedigreeAnalysis probabilityTest probabilityTest,FAData-method sliceAge
Basic pedigree utilities	cliques,missing-method connectedSubgraph countGenerations countGenerations,data.frame-method countGenerations,FAData-method countGenerations,pedigree-method countGenerations,pedigreeList-method estimateGenerations estimateGenerations,data.frame-method estimateGenerations,FAData-method estimateGenerations,pedigree-method estimateGenerations,pedigreeList-method findFounders findFounders,data.frame-method findFounders,FAData-method findFounders,pedigree-method findFounders,pedigreeList-method generationsFrom generationsFrom,data.frame-method generationsFrom,FAData-method generationsFrom,pedigree-method generationsFrom,pedigreeList-method getAncestors getAncestors,data.frame-method getAncestors,FAData-method getAncestors,pedigree-method getAncestors,pedigreeList-method getChildren getChildren,data.frame-method getChildren,FAData-method getChildren,pedigree-method getChildren,pedigreeList-method getCommonAncestor getCommonAncestor,data.frame-method getCommonAncestor,FAData-method getCommonAncestor,pedigree-method getCommonAncestor,pedigreeList-method getFounders getFounders,data.frame-method getFounders,FAData-method getMissingMate getMissingMate,data.frame-method getMissingMate,FAData-method getMissingMate,pedigree-method getMissingMate,pedigreeList-method getSiblings getSiblings,data.frame-method getSiblings,FAData-method getSiblings,pedigree-method getSiblings,pedigreeList-method getSingletons getSingletons,data.frame-method getSingletons,FAData-method ped2graph PedigreeUtils removeSingletons removeSingletons,data.frame-method removeSingletons,FAData-method shareKinship shareKinship,FAData-method subPedigree
Pedigree plotting functions	doPlotPed switchPlotfun