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.

AuthorJ. Rainer, D. Taliun, C.X. Weichenberger
Date of publicationNone
MaintainerJohannes Rainer <johannes.rainer@eurac.edu>
LicenseMIT + file LICENSE
Version1.2.1
https://github.com/jotsetung/FamAgg

View on Bioconductor

Functions

$ Man page
affectedIndividuals Man page
affectedIndividuals,FAData-method Man page
affectedKinshipGroups Man page
affectedKinshipGroups,FAKinGroupResults-method Man page
age Man page
age<- Man page
age<-,FAData-method Man page
age,FAData-method Man page
buildPed Man page
buildPed,FAData-method Man page
buildPed,FAKinGroupResults-method Man page
buildPed,FAProbResults-method Man page
cliqueAndTrait Man page
cliqueAndTrait,FAProbResults-method Man page
cliques Man page
cliques<- Man page
cliques<-,FAProbResults-method Man page
cliques,FAProbResults-method Man page
cliques,missing-method Man page
connectedSubgraph Man page
countGenerations Man page
countGenerations,data.frame-method Man page
countGenerations,FAData-method Man page
countGenerations,pedigreeList-method Man page
countGenerations,pedigree-method Man page
doPlotPed Man page
estimateGenerations Man page
estimateGenerations,data.frame-method Man page
estimateGenerations,FAData-method Man page
estimateGenerations,pedigreeList-method Man page
estimateGenerations,pedigree-method Man page
estimateTimeAtRisk Man page
export Man page
export,FAData-method Man page
factor2matrix Man page
FAData Man page
[,FAData,ANY,ANY,ANY-method Man page
[,FAData,ANY-method Man page
FAData-class Man page
$,FAData-method Man page
FAGenIndexResults Man page
[,FAGenIndexResults,ANY,ANY,ANY-method Man page
[,FAGenIndexResults,ANY-method Man page
FAGenIndexResults-class Man page
FAIncidenceRateResults Man page
[,FAIncidenceRateResults,ANY,ANY,ANY-method Man page
[,FAIncidenceRateResults,ANY-method Man page
FAIncidenceRateResults-class Man page
$,FAIncidenceRateResults-method Man page
FAKinGroupResults Man page
[,FAKinGroupResults,ANY,ANY,ANY-method Man page
[,FAKinGroupResults,ANY-method Man page
FAKinGroupResults-class Man page
FAKinSumResults Man page
[,FAKinSumResults,ANY,ANY,ANY-method Man page
[,FAKinSumResults,ANY-method Man page
FAKinSumResults-class Man page
familialIncidenceRate Man page
familialIncidenceRate,FAData-method Man page
familialIncidenceRate,FAIncidenceRateResults-method Man page
familialIncidenceRateTest Man page
familialIncidenceRateTest,FAData-method Man page
family Man page
family,FAData-method Man page
FAProbResults Man page
[,FAProbResults,ANY,ANY,ANY-method Man page
[,FAProbResults,ANY-method Man page
FAProbResults-class Man page
FAStdIncidenceRateResults Man page
[,FAStdIncidenceRateResults,ANY,ANY,ANY-method Man page
[,FAStdIncidenceRateResults,ANY-method Man page
FAStdIncidenceRateResults-class Man page
$,FAStdIncidenceRateResults-method Man page
findFounders Man page
findFounders,data.frame-method Man page
findFounders,FAData-method Man page
findFounders,pedigreeList-method Man page
findFounders,pedigree-method Man page
fsir Man page
fsir,FAData-method Man page
fsir,FAStdIncidenceRateResults-method Man page
fsirTest Man page
fsirTest,FAData-method Man page
genealogicalIndexTest Man page
genealogicalIndexTest,FAData-method Man page
generationsFrom Man page
generationsFrom,data.frame-method Man page
generationsFrom,FAData-method Man page
generationsFrom,pedigreeList-method Man page
generationsFrom,pedigree-method Man page
getAll Man page
getAll,data.frame-method Man page
getAll,FAData-method Man page
getAll,pedigreeList-method Man page
getAll,pedigree-method Man page
getAncestors Man page
getAncestors,data.frame-method Man page
getAncestors,FAData-method Man page
getAncestors,pedigreeList-method Man page
getAncestors,pedigree-method Man page
getChildren Man page
getChildren,data.frame-method Man page
getChildren,FAData-method Man page
getChildren,pedigreeList-method Man page
getChildren,pedigree-method Man page
getCommonAncestor Man page
getCommonAncestor,data.frame-method Man page
getCommonAncestor,FAData-method Man page
getCommonAncestor,pedigreeList-method Man page
getCommonAncestor,pedigree-method Man page
getExternalMatched Man page
getExternalMatched,data.frame-method Man page
getExternalMatched,FAData-method Man page
getExternalMatched,pedigreeList-method Man page
getExternalMatched,pedigree-method Man page
getFounders Man page
getFounders,data.frame-method Man page
getFounders,FAData-method Man page
getGenerationMatched Man page
getGenerationMatched,data.frame-method Man page
getGenerationMatched,FAData-method Man page
getGenerationMatched,pedigreeList-method Man page
getGenerationMatched,pedigree-method Man page
getGenerationSexMatched Man page
getGenerationSexMatched,data.frame-method Man page
getGenerationSexMatched,FAData-method Man page
getGenerationSexMatched,pedigreeList-method Man page
getGenerationSexMatched,pedigree-method Man page
getMissingMate Man page
getMissingMate,data.frame-method Man page
getMissingMate,FAData-method Man page
getMissingMate,pedigreeList-method Man page
getMissingMate,pedigree-method Man page
getSexMatched Man page
getSexMatched,data.frame-method Man page
getSexMatched,FAData-method Man page
getSexMatched,pedigreeList-method Man page
getSexMatched,pedigree-method Man page
getSiblings Man page
getSiblings,data.frame-method Man page
getSiblings,FAData-method Man page
getSiblings,pedigreeList-method Man page
getSiblings,pedigree-method Man page
getSingletons Man page
getSingletons,data.frame-method Man page
getSingletons,FAData-method Man page
independentGroupCount Man page
independentGroupCount,FAKinGroupResults-method Man page
kinship Man page
kinship,FAData-method Man page
kinshipGroupTest Man page
kinshipGroupTest,FAData-method Man page
kinshipSumTest Man page
kinshipSumTest,FAData-method Man page
lambda Man page
lambda,FAStdIncidenceRateResults-method Man page
ped2graph Man page
pedigree Man page
pedigree<- Man page
PedigreeAnalysis Man page
pedigree<-,FAData-method Man page
pedigree,FAData-method Man page
pedigree,missing-method Man page
pedigreeSize Man page
pedigreeSize,FAData-method Man page
PedigreeUtils Man page
phenotypedIndividuals Man page
phenotypedIndividuals,FAData-method Man page
plotPed Man page
plotPed,FAData-method Man page
plotPed,FAGenIndexResults-method Man page
plotPed,FAIncidenceRateResults-method Man page
plotPed,FAKinGroupResults-method Man page
plotPed,FAKinSumResults-method Man page
plotPed,FAProbResults-method Man page
plotPed,FAStdIncidenceRateResults-method Man page
plotRes Man page
plotRes,FAGenIndexResults-method Man page
plotRes,FAIncidenceRateResults-method Man page
plotRes,FAKinGroupResults-method Man page
plotRes,FAKinSumResults-method Man page
plotRes,FAStdIncidenceRateResults-method Man page
probabilityTest Man page
probabilityTest,FAData-method Man page
removeSingletons Man page
result Man page
result,FAGenIndexResults-method Man page
result,FAIncidenceRateResults-method Man page
result,FAKinGroupResults-method Man page
result,FAKinSumResults-method Man page
result,FAProbResults-method Man page
result,FAStdIncidenceRateResults-method Man page
resultForId Man page
resultForId,FAStdIncidenceRateResults-method Man page
runSimulation Man page
runSimulation,FAGenIndexResults-method Man page
runSimulation,FAIncidenceRateResults-method Man page
runSimulation,FAKinGroupResults-method Man page
runSimulation,FAKinSumResults-method Man page
runSimulation,FAProbResults-method Man page
runSimulation,FAStdIncidenceRateResults-method Man page
shareKinship Man page
shareKinship,FAData-method Man page
shareKinship,FAKinGroupResults-method Man page
shareKinship,FAProbResults-method Man page
show Man page
show,FAData-method Man page
sliceAge Man page
subPedigree Man page
switchPlotfun Man page
timeAtRisk Man page
timeAtRisk<- Man page
timeAtRisk<-,FAIncidenceRateResults-method Man page
timeAtRisk,FAIncidenceRateResults-method Man page
timeInStrata Man page
timeInStrata,FAStdIncidenceRateResults-method Man page
trait Man page
trait<- Man page
traitByClique Man page
traitByClique,FAProbResults-method Man page
trait<-,FAData-method Man page
trait,FAData-method Man page
trait<-,FAGenIndexResults-method Man page
trait<-,FAIncidenceRateResults-method Man page
trait<-,FAKinGroupResults-method Man page
trait<-,FAKinSumResults-method Man page
trait<-,FAProbResults-method Man page
trait<-,FAStdIncidenceRateResults-method Man page

Files

FamAgg/DESCRIPTION
FamAgg/LICENSE
FamAgg/NAMESPACE
FamAgg/R
FamAgg/R/Classes.R FamAgg/R/Constructors.R FamAgg/R/Generics.R FamAgg/R/Methods-FAData.R FamAgg/R/Methods-FAGenIndexResults.R FamAgg/R/Methods-FAIncidenceRateResults.R FamAgg/R/Methods-FAKinGroupResults.R FamAgg/R/Methods-FAKinSumResults.R FamAgg/R/Methods-FAProbResults.R FamAgg/R/Methods-FAStdIncidenceRateResults.R FamAgg/R/Methods.R FamAgg/R/import-export.R FamAgg/R/matched-controls.R FamAgg/R/plotting-functions.R FamAgg/R/utils.R FamAgg/R/zzz.R
FamAgg/build
FamAgg/build/vignette.rds
FamAgg/inst
FamAgg/inst/CITATION
FamAgg/inst/NEWS
FamAgg/inst/doc
FamAgg/inst/doc/FamAgg.R
FamAgg/inst/doc/FamAgg.Rmd
FamAgg/inst/doc/FamAgg.html
FamAgg/inst/perl
FamAgg/inst/perl/HaploPainter1.043.pl
FamAgg/inst/txt
FamAgg/inst/txt/Large-cliques.txt
FamAgg/inst/txt/Large.ped
FamAgg/inst/txt/minnbreast_default_cliques.txt
FamAgg/inst/txt/minnbreastsub-bad.ped.gz
FamAgg/inst/txt/minnbreastsub.ped.gz
FamAgg/inst/txt/minnbreastsub.txt
FamAgg/inst/unitTests
FamAgg/inst/unitTests/test_FAData.R
FamAgg/inst/unitTests/test_controls_N_sampling.R
FamAgg/inst/unitTests/test_fsir.R
FamAgg/inst/unitTests/test_genealogical_index.R
FamAgg/inst/unitTests/test_incidence_ratio.R
FamAgg/inst/unitTests/test_internals.R
FamAgg/inst/unitTests/test_kinship_group.R
FamAgg/inst/unitTests/test_kinship_sum.R
FamAgg/inst/unitTests/test_plotting.R
FamAgg/inst/unitTests/test_probability.R
FamAgg/inst/unitTests/test_utilities.R
FamAgg/man
FamAgg/man/FAData-analysis.Rd FamAgg/man/FAData.Rd FamAgg/man/FAGenIndexResults.Rd FamAgg/man/FAIncidenceRateResults.Rd FamAgg/man/FAKinGroupResults.Rd FamAgg/man/FAKinSumResults.Rd FamAgg/man/FAProbResults.Rd FamAgg/man/FAStdIncidenceRateResults.Rd FamAgg/man/Pedigree-utils.Rd FamAgg/man/defineControls.Rd FamAgg/man/plotting-functions.Rd
FamAgg/tests
FamAgg/tests/runTests.R
FamAgg/vignettes
FamAgg/vignettes/FamAgg.Rmd
FamAgg/vignettes/FamAgg.org
FamAgg/vignettes/biomed-central.csl
FamAgg/vignettes/references.bib

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