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GENLIB (version 1.1.10)

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

334

Version

1.1.10

License

GPL (>= 2)

Maintainer

Marie-Helene Roy-Gagnon

Last Published

February 19th, 2024

Functions in GENLIB (1.1.10)

gen.climbPAR

Internal function used by gen.findMRCA
gen.lineages

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

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

Variance of genealogical implex
gen.occ

Ancestor occurences
gen.nowomen

Number of women
gen.genealogy

Create object of class GLgen
gen.simuHaplo_traceback

Trace inheritance path for results from gene dropping simulation
geneaJi

Highly inbred pedigree
genea140

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

Get id numbers of parents
gen.phi

Kinship coefficient
gen.simuSet

Gene dropping simulations with specified transmission probabilities
gen.meangendepth

Expected Genealogical Depth
gen.depth

Genealogy depth
gen.simuSampleFreq

Gene dropping simulations - Frequencies
gen.meangendepthVar

Variance of genealogical depth
pop140

Population of origin of the 140 Quebec samples
gen.half.founder

Get half-founder id numbers
gen.getAncestorsPAR

Internal function used by gen.findMRCA
gen.genout

Create pedigree data
gen.phiMean

Average kinship
gen.noind

Number of individuals
gen.phiCI

Average kinship confidence interval
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.simuHaplo_IBD_compare

Compare proband haplotypes for IBD sharing
gen.simuHaplo

Gene dropping simulations - haplotypes
gen.nomen

Number of men
gen.graph

Pedigree graphical tool
gen.rec

Ancestors coverage
gen.implex

Genealogical implex
gen.nochildren

Number of children
gen.findDistance

Minimum genetic distance between two individuals
gen.findFounders

Find common founder ancestors
gen.simuProb

Gene dropping simulations - Probabilities
gen.getFoundersPAR

Internal function used by gen.findFounders
gen.sibship

Get id numbers of siblings
gen.simuSample

Gene dropping simulations - Sample
gen.min

Minimum number of generations
gen.pro

Get proband id numbers
gen.phiOver

Kinship above threshold
Classes of GLgroup handling

Classes "GLmultiPhiGroup" "GLmultiPhiGroupSingle" "GLmultiFGroup" "GLmultiFGroupSingle" "GLCGMatrixGroupSingle"
gen.completeness

Completeness
Classes of basic handling of genealogy data

Classes "GLmultiVector" "GLmultiArray4" "GLmultiMatrix" "GLmultiNumber"
GLgroup-class

Class "GLgroup"
gen.findMRCA

Finding most recent common ancestors, MRCAs
gen.children

Get id numbers of children
GLgen-class

Class "GLgen"
GLmultiList-class

Class "GLmultiList"
gen.founder

Get founder id numbers
gen.gc

Genetic contribution of ancestors
gen.branching

Genealogy subset
gen.completenessVar

Variance of completeness index
gen.max

Maximum number of generations
gen.mean

Mean number of generations
gen.f

Inbreeding coefficient