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GENLIB (version 1.1.9)

Genealogical Data Analysis

Description

Genealogical data analysis including descriptive statistics (e.g., kinship and inbreeding coefficients) and gene-dropping simulations. See: "GENLIB: an R package for the analysis of genealogical data" Gauvin et al. (2015) .

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Version

Install

install.packages('GENLIB')

Monthly Downloads

342

Version

1.1.9

License

GPL (>= 2)

Maintainer

Marie-Helene Roy-Gagnon

Last Published

January 17th, 2023

Functions in GENLIB (1.1.9)

gen.children

Get id numbers of children
gen.completenessVar

Variance of completeness index
gen.gc

Genetic contribution of ancestors
gen.branching

Genealogy subset
gen.depth

Genealogy depth
gen.founder

Get founder id numbers
gen.findMRCA

Finding most recent common ancestors, MRCAs
gen.find.Min.Distance.MRCA

Finds the minimum distances between pairs of individuals given a set of ancestors.
gen.fCI

Average inbreeding coefficient confidence interval
gen.findDistance

Minimum genetic distance between two individuals
gen.f

Inbreeding coefficient
gen.findFounders

Find common founder ancestors
gen.genealogy

Create object of class GLgen
gen.half.founder

Get half-founder id numbers
gen.implex

Genealogical implex
gen.getAncestorsPAR

Internal function used by gen.findMRCA
gen.getFoundersPAR

Internal function used by gen.findFounders
gen.graph

Pedigree graphical tool
gen.nochildren

Number of children
gen.occ

Ancestor occurences
gen.genout

Create pedigree data
gen.lineages

Create object of class GLgen for maternal or paternal lineages
gen.max

Maximum number of generations
gen.nomen

Number of men
gen.min

Minimum number of generations
gen.parent

Get id numbers of parents
gen.implexVar

Variance of genealogical implex
gen.meangendepthVar

Variance of genealogical depth
gen.nowomen

Number of women
gen.simuHaplo_convert

Convert proband simulation results into sequence data given founder haplotypes
gen.simuHaplo_IBD_compare

Compare proband haplotypes for IBD sharing
gen.pro

Get proband id numbers
gen.rec

Ancestors coverage
gen.noind

Number of individuals
gen.phiMean

Average kinship
gen.mean

Mean number of generations
gen.phiCI

Average kinship confidence interval
gen.phi

Kinship coefficient
gen.simuProb

Gene dropping simulations - Probabilities
gen.simuHaplo_traceback

Trace inheritance path for results from gene dropping simulation
gen.phiOver

Kinship above threshold
gen.simuSampleFreq

Gene dropping simulations - Frequencies
gen.simuSample

Gene dropping simulations - Sample
geneaJi

Highly inbred pedigree
pop140

Population of origin of the 140 Quebec samples
gen.simuHaplo

Gene dropping simulations - haplotypes
gen.sibship

Get id numbers of siblings
gen.meangendepth

Expected Genealogical Depth
genea140

Genealogical information for 140 individuals from the Quebec Reference Sample
gen.simuSet

Gene dropping simulations with specified transmission probabilities
Classes of GLgroup handling

Classes "GLmultiPhiGroup" "GLmultiPhiGroupSingle" "GLmultiFGroup" "GLmultiFGroupSingle" "GLCGMatrixGroupSingle"
GLgen-class

Class "GLgen"
GLgroup-class

Class "GLgroup"
GLmultiList-class

Class "GLmultiList"
Classes of basic handling of genealogy data

Classes "GLmultiVector" "GLmultiArray4" "GLmultiMatrix" "GLmultiNumber"
GenlibR-package

Genealogical Data Analysis
gen.climbPAR

Internal function used by gen.findMRCA
gen.completeness

Completeness