FamAgg: Pedigree Analysis and Familial Aggregation
Version 1.4.1

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
Bioconductor views Genetics
Date of publicationNone
MaintainerJohannes Rainer <johannes.rainer@eurac.edu>
LicenseMIT + file LICENSE
Version1.4.1
URL https://github.com/jotsetung/FamAgg
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("FamAgg")

Getting started

Pedigree Analysis and Familial Aggregation

Popular man pages

FAData: Pedigree data information
FAData-analysis: Pedigree analysis and familial aggregation methods
FAGenIndexResults: Genealogical Index
FAKinGroupResults: Kinship group test
FAKinSumResults: Kinship sum test
FAStdIncidenceRateResults: Familial Standardized Incidence Rate
Pedigree-utils: Basic pedigree utilities
See all...

All man pages Function index File listing

Man pages

defineControls: Define sets of control individuals for one or more given...
FAData: Pedigree data information
FAData-analysis: Pedigree analysis and familial aggregation methods
FAGenIndexResults: Genealogical Index
FAIncidenceRateResults: Familial Incidence Rate
FAKinGroupResults: Kinship group test
FAKinSumResults: Kinship sum test
FAProbResults: Probability test
FAStdIncidenceRateResults: Familial Standardized Incidence Rate
Pedigree-utils: Basic pedigree utilities
plotting-functions: Pedigree plotting functions

Functions

$ Man page
$,FAData-method Man page
$,FAIncidenceRateResults-method Man page
$,FAStdIncidenceRateResults-method Man page
FAData Man page Source code
FAData-class Man page
FAGenIndexResults Man page
FAGenIndexResults-class Man page
FAIncidenceRateResults Man page
FAIncidenceRateResults-class Man page
FAKinGroupResults Man page
FAKinGroupResults-class Man page
FAKinSumResults Man page
FAKinSumResults-class Man page
FAProbResults Man page
FAProbResults-class Man page
FAStdIncidenceRateResults Man page
FAStdIncidenceRateResults-class Man page
FR Source code
FRSimulation Source code
PedigreeAnalysis Man page
PedigreeUtils Man page
[,FAData,ANY,ANY,ANY-method Man page
[,FAData,ANY-method Man page
[,FAGenIndexResults,ANY,ANY,ANY-method Man page
[,FAGenIndexResults,ANY-method Man page
[,FAIncidenceRateResults,ANY,ANY,ANY-method Man page
[,FAIncidenceRateResults,ANY-method Man page
[,FAKinGroupResults,ANY,ANY,ANY-method Man page
[,FAKinGroupResults,ANY-method Man page
[,FAKinSumResults,ANY,ANY,ANY-method Man page
[,FAKinSumResults,ANY-method Man page
[,FAProbResults,ANY,ANY,ANY-method Man page
[,FAProbResults,ANY-method Man page
[,FAStdIncidenceRateResults,ANY,ANY,ANY-method Man page
[,FAStdIncidenceRateResults,ANY-method Man page
affectedIndividuals Man page
affectedIndividuals,FAData-method Man page
affectedKinshipGroups Man page
affectedKinshipGroups,FAKinGroupResults-method Man page
age Man page
age,FAData-method Man page
age<- Man page
age<-,FAData-method Man page
bg.ks.distr Source code
bg.ks.distr.strat Source code
bracketSubset Source code
buildHaplopaintDataframe Source code
buildPed Man page
buildPed,FAData-method Man page
buildPed,FAKinGroupResults-method Man page
buildPed,FAProbResults-method Man page
buildPedigree Source code
checkArgAreTwins Source code
checkArgConsanguineous Source code
checkArgNumericLogical Source code
checkHaplopaintRequirements Source code
checkLabels Source code
checkPedCol Source code
checkRowindex Source code
checkTransformNumeric Source code
cliqueAndTrait Man page
cliqueAndTrait,FAProbResults-method Man page
cliques Man page
cliques,FAProbResults-method Man page
cliques,missing-method Man page
cliques<- Man page
cliques<-,FAProbResults-method Man page
connectedSubgraph Man page Source code
countGenerations Man page
countGenerations,FAData-method Man page
countGenerations,data.frame-method Man page
countGenerations,pedigree-method Man page
countGenerations,pedigreeList-method Man page
df2ped Source code
doCountGenerations Source code
doEstimateGenerationsFor2 Source code
doFindFounders Source code
doFindFoundersForId Source code
doFsir Source code
doFsirSimulation Source code
doGetAll Source code
doGetAncestors Source code
doGetChildren Source code
doGetCommonAncestor Source code
doGetExternalMatched Source code
doGetFounders Source code
doGetGenerationFrom2 Source code
doGetGenerationMatched Source code
doGetGenerationSexMatched Source code
doGetMissingMate Source code
doGetSexMatched Source code
doGetSiblings Source code
doGetSingletons Source code
doImport Source code
doImportFam Source code
doImportGeneric Source code
doImportPed Source code
doPlotPed Man page Source code
doProcessDf2Ped Source code
doProcessPed2Df Source code
doPrunePed Source code
doShareKinship Source code
estimateGenerations Man page
estimateGenerations,FAData-method Man page
estimateGenerations,data.frame-method Man page
estimateGenerations,pedigree-method Man page
estimateGenerations,pedigreeList-method Man page
estimateTimeAtRisk Man page Source code
export Man page
export,FAData-method Man page
factor2matrix Man page Source code
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
fileExtension Source code
findFounders Man page
findFounders,FAData-method Man page
findFounders,data.frame-method Man page
findFounders,pedigree-method Man page
findFounders,pedigreeList-method Man page
fsir Man page
fsir,FAData-method Man page
fsir,FAStdIncidenceRateResults-method Man page
fsirTest Man page
fsirTest,FAData-method Man page
genIndex Source code
genealogicalIndexTest Man page
genealogicalIndexTest,FAData-method Man page
generationsFrom Man page
generationsFrom,FAData-method Man page
generationsFrom,data.frame-method Man page
generationsFrom,pedigree-method Man page
generationsFrom,pedigreeList-method Man page
getAll Man page
getAll,FAData-method Man page
getAll,data.frame-method Man page
getAll,pedigree-method Man page
getAll,pedigreeList-method Man page
getAllSibsNMates Source code
getAncestors Man page
getAncestors,FAData-method Man page
getAncestors,data.frame-method Man page
getAncestors,pedigree-method Man page
getAncestors,pedigreeList-method Man page
getChildren Man page
getChildren,FAData-method Man page
getChildren,data.frame-method Man page
getChildren,pedigree-method Man page
getChildren,pedigreeList-method Man page
getCommonAncestor Man page
getCommonAncestor,FAData-method Man page
getCommonAncestor,data.frame-method Man page
getCommonAncestor,pedigree-method Man page
getCommonAncestor,pedigreeList-method Man page
getExternalMatched Man page
getExternalMatched,FAData-method Man page
getExternalMatched,data.frame-method Man page
getExternalMatched,pedigree-method Man page
getExternalMatched,pedigreeList-method Man page
getFounders Man page
getFounders,FAData-method Man page
getFounders,data.frame-method Man page
getGenerationMatched Man page
getGenerationMatched,FAData-method Man page
getGenerationMatched,data.frame-method Man page
getGenerationMatched,pedigree-method Man page
getGenerationMatched,pedigreeList-method Man page
getGenerationSexMatched Man page
getGenerationSexMatched,FAData-method Man page
getGenerationSexMatched,data.frame-method Man page
getGenerationSexMatched,pedigree-method Man page
getGenerationSexMatched,pedigreeList-method Man page
getMissingMate Man page
getMissingMate,FAData-method Man page
getMissingMate,data.frame-method Man page
getMissingMate,pedigree-method Man page
getMissingMate,pedigreeList-method Man page
getParents Source code
getSexMatched Man page
getSexMatched,FAData-method Man page
getSexMatched,data.frame-method Man page
getSexMatched,pedigree-method Man page
getSexMatched,pedigreeList-method Man page
getSiblings Man page
getSiblings,FAData-method Man page
getSiblings,data.frame-method Man page
getSiblings,pedigree-method Man page
getSiblings,pedigreeList-method Man page
getSingletons Man page
getSingletons,FAData-method Man page
getSingletons,data.frame-method Man page
haplopaint Source code
independentGroupCount Man page
independentGroupCount,FAKinGroupResults-method Man page
infOrZero Source code
kinship Man page
kinship,FAData-method Man page
kinshipGroupTest Man page
kinshipGroupTest,FAData-method Man page
kinshipSumTest Man page
kinshipSumTest,FAData-method Man page
ks2paint Source code
lambda Man page
lambda,FAStdIncidenceRateResults-method Man page
noColNames Source code
onAttach Source code
onLoad Source code
ped2df Source code
ped2graph Man page Source code
pedigree Man page
pedigree,FAData-method Man page
pedigree,missing-method Man page
pedigree<- Man page
pedigree<-,FAData-method Man page
pedigreeSize Man page
pedigreeSize,FAData-method 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
plotPedForKinshipResult Source code
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 Source code
removeSingletons,FAData-method Man page
removeSingletons,data.frame-method 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
sanitizePed Source code
sanitizeSex Source code
setOptions Source code
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
significant.individuals.althyp Source code
sliceAge Man page Source code
subPedigree Man page Source code
switchPlotfun Man page Source code
timeAtRisk Man page
timeAtRisk,FAIncidenceRateResults-method Man page
timeAtRisk<- Man page
timeAtRisk<-,FAIncidenceRateResults-method Man page
timeInStrata Man page
timeInStrata,FAStdIncidenceRateResults-method Man page
trait Man page
trait,FAData-method Man page
trait<- 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
traitByClique Man page
traitByClique,FAProbResults-method Man page
validateFAData Source code
writePed Source code

Files

DESCRIPTION
LICENSE
NAMESPACE
R
R/Classes.R
R/Constructors.R
R/Generics.R
R/Methods-FAData.R
R/Methods-FAGenIndexResults.R
R/Methods-FAIncidenceRateResults.R
R/Methods-FAKinGroupResults.R
R/Methods-FAKinSumResults.R
R/Methods-FAProbResults.R
R/Methods-FAStdIncidenceRateResults.R
R/Methods.R
R/import-export.R
R/matched-controls.R
R/plotting-functions.R
R/utils.R
R/zzz.R
build
build/vignette.rds
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/FamAgg.R
inst/doc/FamAgg.Rmd
inst/doc/FamAgg.html
inst/perl
inst/perl/HaploPainter1.043.pl
inst/txt
inst/txt/Large-cliques.txt
inst/txt/Large.ped
inst/txt/minnbreast_default_cliques.txt
inst/txt/minnbreastsub-bad.ped.gz
inst/txt/minnbreastsub.ped.gz
inst/txt/minnbreastsub.txt
inst/unitTests
inst/unitTests/test_FAData.R
inst/unitTests/test_controls_N_sampling.R
inst/unitTests/test_fsir.R
inst/unitTests/test_genealogical_index.R
inst/unitTests/test_incidence_ratio.R
inst/unitTests/test_internals.R
inst/unitTests/test_kinship_group.R
inst/unitTests/test_kinship_sum.R
inst/unitTests/test_plotting.R
inst/unitTests/test_probability.R
inst/unitTests/test_utilities.R
man
man/FAData-analysis.Rd
man/FAData.Rd
man/FAGenIndexResults.Rd
man/FAIncidenceRateResults.Rd
man/FAKinGroupResults.Rd
man/FAKinSumResults.Rd
man/FAProbResults.Rd
man/FAStdIncidenceRateResults.Rd
man/Pedigree-utils.Rd
man/defineControls.Rd
man/plotting-functions.Rd
tests
tests/runTests.R
vignettes
vignettes/FamAgg.Rmd
vignettes/FamAgg.org
vignettes/biomed-central.csl
vignettes/references.bib
FamAgg documentation built on May 20, 2017, 9:44 p.m.

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