Pedigree Analysis and Familial Aggregation

Documentation for package ‘FamAgg’ version 1.30.0

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-- 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