Pedigree Analysis and Familial Aggregation

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Documentation for package ‘FamAgg’ version 1.18.0

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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
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