R: Genealogical Data Analysis

# Genealogical Data Analysis

## Documentation for package ‘GENLIB’ version 1.1.10

- DESCRIPTION file

## Help Pages

depth-method | Class '"GLgen"'
depth-method | Classes '"GLmultiVector"' '"GLmultiArray4"' '"GLmultiMatrix"' '"GLmultiNumber"'
Dim-method | Classes '"GLmultiPhiGroup"' '"GLmultiPhiGroupSingle"' '"GLmultiFGroup"' '"GLmultiFGroupSingle"' '"GLCGMatrixGroupSingle"'
Dim-method | Classes '"GLmultiVector"' '"GLmultiArray4"' '"GLmultiMatrix"' '"GLmultiNumber"'
gen.branching | Genealogy subset
gen.children | Get id numbers of children
gen.climbPAR | Internal function used by gen.findMRCA
gen.completeness | Completeness
gen.completenessVar | Variance of completeness index
gen.depth | Genealogy depth
gen.f | Inbreeding coefficient
gen.fCI | Average inbreeding coefficient confidence interval
gen.find.Min.Distance.MRCA | Finds the minimum distances between pairs of individuals given a set of ancestors.
gen.findDistance | Minimum genetic distance between two individuals
gen.findFounders | Find common founder ancestors
gen.findMRCA | Finding most recent common ancestors, MRCAs
gen.founder | Get founder id numbers
gen.gc | Genetic contribution of ancestors
gen.genealogy | Create object of class GLgen
gen.genout | Create pedigree data
gen.getAncestorsPAR | Internal function used by gen.findMRCA
gen.getFoundersPAR | Internal function used by gen.findFounders
gen.graph | Pedigree graphical tool
gen.half.founder | Get half-founder id numbers
gen.implex | Genealogical implex
gen.implexVar | Variance of genealogical implex
gen.lineages | Create object of class GLgen for maternal or paternal lineages
gen.max | Maximum number of generations
gen.mean | Mean number of generations
gen.meangendepth | Expected Genealogical Depth
gen.meangendepthVar | Variance of genealogical depth
gen.min | Minimum number of generations
gen.nochildren | Number of children
gen.noind | Number of individuals
gen.nomen | Number of men
gen.nowomen | Number of women
gen.occ | Ancestor occurences
gen.parent | Get id numbers of parents
gen.phi | Kinship coefficient
gen.phiCI | Average kinship confidence interval
gen.phiMean | Average kinship
gen.phiOver | Kinship above threshold
gen.pro | Get proband id numbers
gen.rec | Ancestors coverage
gen.sibship | Get id numbers of siblings
gen.simuHaplo | Gene dropping simulations - haplotypes
gen.simuHaplo_convert | Convert proband simulation results into sequence data given founder haplotypes
gen.simuHaplo_IBD_compare | Compare proband haplotypes for IBD sharing
gen.simuHaplo_traceback | Trace inheritance path for results from gene dropping simulation
gen.simuProb | Gene dropping simulations - Probabilities
gen.simuSample | Gene dropping simulations - Sample
gen.simuSampleFreq | Gene dropping simulations - Frequencies
gen.simuSet | Gene dropping simulations with specified transmission probabilities
genea140 | Genealogical information for 140 individuals from the Quebec Reference Sample
geneaJi | Highly inbred pedigree
GLCGMatrixGroupSingle-class | Classes '"GLmultiPhiGroup"' '"GLmultiPhiGroupSingle"' '"GLmultiFGroup"' '"GLmultiFGroupSingle"' '"GLCGMatrixGroupSingle"'
GLgen-class | Class '"GLgen"'
GLgroup-class | Class '"GLgroup"'
GLmultiArray4-class | Classes '"GLmultiVector"' '"GLmultiArray4"' '"GLmultiMatrix"' '"GLmultiNumber"'
GLmultiFGroup-class | Classes '"GLmultiPhiGroup"' '"GLmultiPhiGroupSingle"' '"GLmultiFGroup"' '"GLmultiFGroupSingle"' '"GLCGMatrixGroupSingle"'
GLmultiFGroupSingle-class | Classes '"GLmultiPhiGroup"' '"GLmultiPhiGroupSingle"' '"GLmultiFGroup"' '"GLmultiFGroupSingle"' '"GLCGMatrixGroupSingle"'
GLmultiList-class | Class '"GLmultiList"'
GLmultiMatrix-class | Classes '"GLmultiVector"' '"GLmultiArray4"' '"GLmultiMatrix"' '"GLmultiNumber"'
GLmultiNumber-class | Classes '"GLmultiVector"' '"GLmultiArray4"' '"GLmultiMatrix"' '"GLmultiNumber"'
GLmultiPhiGroup-class | Classes '"GLmultiPhiGroup"' '"GLmultiPhiGroupSingle"' '"GLmultiFGroup"' '"GLmultiFGroupSingle"' '"GLCGMatrixGroupSingle"'
GLmultiPhiGroupSingle-class | Classes '"GLmultiPhiGroup"' '"GLmultiPhiGroupSingle"' '"GLmultiFGroup"' '"GLmultiFGroupSingle"' '"GLCGMatrixGroupSingle"'
GLmultiVector-class | Classes '"GLmultiVector"' '"GLmultiArray4"' '"GLmultiMatrix"' '"GLmultiNumber"'
initialize-method | Class '"GLgen"'
initialize-method | Class '"GLgroup"'
length-method | Class '"GLgen"'
pop140 | Population of origin of the 140 Quebec samples
[-method | Classes '"GLmultiPhiGroup"' '"GLmultiPhiGroupSingle"' '"GLmultiFGroup"' '"GLmultiFGroupSingle"' '"GLCGMatrixGroupSingle"'
[-method | Class '"GLgroup"'
[-method | Classes '"GLmultiVector"' '"GLmultiArray4"' '"GLmultiMatrix"' '"GLmultiNumber"'
[<--method | Classes '"GLmultiPhiGroup"' '"GLmultiPhiGroupSingle"' '"GLmultiFGroup"' '"GLmultiFGroupSingle"' '"GLCGMatrixGroupSingle"'
[<--method | Classes '"GLmultiVector"' '"GLmultiArray4"' '"GLmultiMatrix"' '"GLmultiNumber"'