# Pedigree Analysis and Familial Aggregation

## Documentation for package ‘FamAgg’ version 1.20.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G K L P R S T misc

## -- A --

affectedIndividuals | Pedigree data information
affectedIndividuals-method | Pedigree data information
affectedKinshipGroups | Kinship group test
affectedKinshipGroups-method | Kinship group test
age | Pedigree data information
age-method | Pedigree data information
age<- | Pedigree data information
age<--method | Pedigree data information

## -- B --

binomialTest | Pedigree analysis and familial aggregation methods
buildPed | Pedigree data information
buildPed-method | Pedigree data information
buildPed-method | Kinship group test
buildPed-method | DEPRECATED: Probability test

## -- C --

cliqueAndTrait | DEPRECATED: Probability test
cliqueAndTrait-method | DEPRECATED: Probability test
cliques | DEPRECATED: Probability test
cliques-method | DEPRECATED: Probability test
cliques-method | Basic pedigree utilities
cliques<- | DEPRECATED: Probability test
cliques<--method | DEPRECATED: Probability test
connectedSubgraph | Basic pedigree utilities
countGenerations | Basic pedigree utilities
countGenerations-method | Basic pedigree utilities

## -- D --

doPlotPed | Pedigree plotting functions

## -- E --

estimateGenerations | Basic pedigree utilities
estimateGenerations-method | Basic pedigree utilities
estimateTimeAtRisk | Pedigree analysis and familial aggregation methods
export | Pedigree data information
export-method | Pedigree data information

## -- F --

FABinTestResults | Binomial test for familial aggregation
FABinTestResults-class | Binomial test for familial aggregation
factor2matrix | Pedigree analysis and familial aggregation methods
FAData | Pedigree data information
FAData-class | Pedigree data information
FAGenIndexResults | Genealogical Index
FAGenIndexResults-class | Genealogical Index
FAIncidenceRateResults | Familial Incidence Rate
FAIncidenceRateResults-class | Familial Incidence Rate
FAKinGroupResults | Kinship group test
FAKinGroupResults-class | Kinship group test
FAKinSumResults | Kinship sum test
FAKinSumResults-class | Kinship sum test
familialIncidenceRate | Pedigree analysis and familial aggregation methods
familialIncidenceRate-method | Pedigree analysis and familial aggregation methods
familialIncidenceRate-method | Familial Incidence Rate
familialIncidenceRateTest | Pedigree analysis and familial aggregation methods
familialIncidenceRateTest-method | Pedigree analysis and familial aggregation methods
family | Pedigree data information
family-method | Pedigree data information
FAProbResults | DEPRECATED: Probability test
FAProbResults-class | DEPRECATED: Probability test
FAStdIncidenceRateResults | Familial Standardized Incidence Rate
FAStdIncidenceRateResults-class | Familial Standardized Incidence Rate
findFounders | Basic pedigree utilities
findFounders-method | Basic pedigree utilities
fsir | Pedigree analysis and familial aggregation methods
fsir-method | Pedigree analysis and familial aggregation methods
fsir-method | Familial Standardized Incidence Rate
fsirTest | Pedigree analysis and familial aggregation methods
fsirTest-method | Pedigree analysis and familial aggregation methods

## -- G --

genealogicalIndexTest | Pedigree analysis and familial aggregation methods
genealogicalIndexTest-method | Pedigree analysis and familial aggregation methods
generationsFrom | Basic pedigree utilities
generationsFrom-method | Basic pedigree utilities
getAll | Define sets of control individuals for one or more given individuals
getAll-method | Define sets of control individuals for one or more given individuals
getAncestors | Basic pedigree utilities
getAncestors-method | Basic pedigree utilities
getChildren | Basic pedigree utilities
getChildren-method | Basic pedigree utilities
getCommonAncestor | Basic pedigree utilities
getCommonAncestor-method | Basic pedigree utilities
getExternalMatched | Define sets of control individuals for one or more given individuals
getExternalMatched-method | Define sets of control individuals for one or more given individuals
getFounders | Basic pedigree utilities
getFounders-method | Basic pedigree utilities
getGenerationMatched | Define sets of control individuals for one or more given individuals
getGenerationMatched-method | Define sets of control individuals for one or more given individuals
getGenerationSexMatched | Define sets of control individuals for one or more given individuals
getGenerationSexMatched-method | Define sets of control individuals for one or more given individuals
getMissingMate | Basic pedigree utilities
getMissingMate-method | Basic pedigree utilities
getSexMatched | Define sets of control individuals for one or more given individuals
getSexMatched-method | Define sets of control individuals for one or more given individuals
getSiblings | Basic pedigree utilities
getSiblings-method | Basic pedigree utilities
getSingletons | Basic pedigree utilities
getSingletons-method | Basic pedigree utilities

## -- K --

kinship | Pedigree data information
kinship-method | Pedigree data information
kinshipGroupTest | Pedigree analysis and familial aggregation methods
kinshipGroupTest-method | Pedigree analysis and familial aggregation methods
kinshipPairs | Extract pairs of individuals matching certain kinship criteria
kinshipSumTest | Pedigree analysis and familial aggregation methods
kinshipSumTest-method | Pedigree analysis and familial aggregation methods

## -- L --

lambda | Familial Standardized Incidence Rate
lambda-method | Familial Standardized Incidence Rate

## -- P --

ped2graph | Basic pedigree utilities
pedigree | Pedigree data information
pedigree-method | Pedigree data information
pedigree<- | Pedigree data information
pedigree<--method | Pedigree data information
PedigreeAnalysis | Pedigree analysis and familial aggregation methods
pedigreeSize | Pedigree data information
pedigreeSize-method | Pedigree data information
PedigreeUtils | Basic pedigree utilities
phenotypedIndividuals | Pedigree data information
phenotypedIndividuals-method | Pedigree data information
plotPed | Pedigree data information
plotPed-method | Pedigree data information
plotPed-method | Genealogical Index
plotPed-method | Familial Incidence Rate
plotPed-method | Kinship group test
plotPed-method | Kinship sum test
plotPed-method | DEPRECATED: Probability test
plotPed-method | Familial Standardized Incidence Rate
plotRes | Genealogical Index
plotRes-method | Genealogical Index
plotRes-method | Familial Incidence Rate
plotRes-method | Kinship group test
plotRes-method | Kinship sum test
plotRes-method | Familial Standardized Incidence Rate
probabilityTest | Pedigree analysis and familial aggregation methods
probabilityTest-method | Pedigree analysis and familial aggregation methods

## -- R --

removeSingletons | Basic pedigree utilities
removeSingletons-method | Basic pedigree utilities
result | DEPRECATED: Probability test
result-method | Binomial test for familial aggregation
result-method | Genealogical Index
result-method | Familial Incidence Rate
result-method | Kinship group test
result-method | Kinship sum test
result-method | DEPRECATED: Probability test
result-method | Familial Standardized Incidence Rate
resultForId | Familial Standardized Incidence Rate
resultForId-method | Familial Standardized Incidence Rate
runSimulation | DEPRECATED: Probability test
runSimulation-method | Genealogical Index
runSimulation-method | Familial Incidence Rate
runSimulation-method | Kinship group test
runSimulation-method | Kinship sum test
runSimulation-method | DEPRECATED: Probability test
runSimulation-method | Familial Standardized Incidence Rate

## -- S --

shareKinship | Basic pedigree utilities
shareKinship-method | Kinship group test
shareKinship-method | DEPRECATED: Probability test
shareKinship-method | Basic pedigree utilities
show | Pedigree data information
show-method | Pedigree data information
sliceAge | Pedigree analysis and familial aggregation methods
subPedigree | Basic pedigree utilities
switchPlotfun | Pedigree plotting functions

## -- T --

timeAtRisk | Familial Incidence Rate
timeAtRisk-method | Familial Incidence Rate
timeAtRisk<- | Familial Incidence Rate
timeAtRisk<--method | Familial Incidence Rate
timeInStrata | Familial Standardized Incidence Rate
timeInStrata-method | Familial Standardized Incidence Rate
trait | Pedigree data information
trait-method | Pedigree data information
trait<- | Pedigree data information
trait<--method | Binomial test for familial aggregation
trait<--method | Pedigree data information
trait<--method | Genealogical Index
trait<--method | Familial Incidence Rate
trait<--method | Kinship group test
trait<--method | Kinship sum test
trait<--method | DEPRECATED: Probability test
trait<--method | Familial Standardized Incidence Rate
traitByClique | DEPRECATED: Probability test
traitByClique-method | DEPRECATED: Probability test

## -- misc --

$ | Pedigree data information
$-method | Pedigree data information
$-method | Familial Incidence Rate
$-method | Familial Standardized Incidence Rate
[-method | Binomial test for familial aggregation
[-method | Pedigree data information
[-method | Genealogical Index
[-method | Familial Incidence Rate
[-method | Kinship group test
[-method | Kinship sum test
[-method | DEPRECATED: Probability test
[-method | Familial Standardized Incidence Rate