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GENLIB (version 1.0.2)

Genealogical Data Analysis

Description

Genealogical data analysis including descriptive statistics (e.g., kinship and inbreeding coefficients) and gene-dropping simulations.

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Version

Install

install.packages('GENLIB')

Monthly Downloads

267

Version

1.0.2

License

GPL (>= 2)

Maintainer

Marie-Helene Roy-Gagnon

Last Published

December 4th, 2014

Functions in GENLIB (1.0.2)

gen.getFoundersPAR

Internal function used by gen.findFounders

gen.children

Get id numbers of children

gen.gc

Genetci contribution of ancestors

gen.genealogy

Create object of class GLgen

gen.fCI

Average inbreeding coefficient confidence interval

gen.entropy

Genelogical entropy (expected genealogical depth)

Classes of GLgroupe handling

Classes "GLmultiPhiGroup" "GLmultiPhiGroupSingle" "GLmultiFGroup" "GLmultiFGroupSingle" "GLCGMatrixGroupSingle"

GenlibR-package

Genealogical Data Analysis

gen.half.founder

Get half-founder id numbers

Classes of basic handling of genealogy data

Classes "GLmultiVector" "GLmultiArray4" "GLmultiMatrix" "GLmultiNumber"

gen.completenessVar

Variance of completeness index

gen.branching

Genealogy subset

GLmultiList-class

Class "GLmultiList"

gen.implex

Genealogical implex

gen.graph

Pedigree graphical tool

gen.findMRCA

Finding most recent common ancestors, MRCAs

gen.findFounders

Find common founder ancestors

gen.getAncestorsPAR

Internal function used by gen.findMRCA

GLgen-class

Class "GLgen"

gen.founder

Get founder id numbers

gen.lineages

Create object of class GLgen for maternal or paternal lineages

gen.grimperPAR

Internal function used by gen.findMRCA

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.depth

Genealogy depth

gen.f

Inbreeding coefficient

gen.implexVar

Variance of genealogical implex

gen.entropyVar

Variance of entropy index

gen.simuSet

Gene dropping simulations with specified transmission probabilities

gen.phiCI

Average kinship confidence interval

gen.pro

Get proband id numbers

gen.min

Minimum number of generations

gen.simuSampleFreq

Gene dropping simulations - Frequencies

gen.phiOver

Kinship above threshold

gen.nochildren

Number of children

gen.noind

Number of individuals

gen.sibship

Get id numbers of siblings

gen.phiMean

Average kinship

gen.parent

Get id numbers of parents

pop140

Population of origin of the 140 Quebec samples

geneaJi

Highly inbred pedigree

gen.mean

Mean number of generations

gen.simuSample

Gene dropping simulations - Sample

gen.simuProb

Gene dropping simulations - Probabilities

Maximum number of generations

gen.nowomen

Number of women

genea140

Genealogical information for 140 individuals from the Quebec Reference Sample