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GENLIB (version 1.0.9)

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

369

Version

1.0.9

License

GPL (>= 2)

Maintainer

Marie-Helene Roy-Gagnon

Last Published

July 19th, 2020

Functions in GENLIB (1.0.9)

GLgroup-class

Class "GLgroup"

Classes of GLgroup handling

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

GenlibR-package

Genealogical Data Analysis

Classes of basic handling of genealogy data

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

Get id numbers of children

gen.completenessVar

Variance of completeness index

GLmultiList-class

Class "GLmultiList"

gen.findFounders

Find common founder ancestors

gen.fCI

Average inbreeding coefficient confidence interval

gen.graph

Pedigree graphical tool

gen.founder

Get founder id numbers

gen.f

Inbreeding coefficient

gen.occ

Ancestor occurences

gen.parent

Get id numbers of parents

gen.genealogy

Create object of class GLgen

gen.phi

Kinship coefficient

gen.gc

Genetic contribution of ancestors

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.findDistance

Minimum genetic distance between two individuals

gen.meangendepthVar

Variance of genealogical depth

gen.half.founder

Get half-founder id numbers

gen.getAncestorsPAR

Internal function used by gen.findMRCA

gen.lineages

Create object of class GLgen for maternal or paternal lineages

gen.max

Maximum number of generations

Mean number of generations

gen.min

Minimum number of generations

gen.implex

Genealogical implex

gen.implexVar

Variance of genealogical implex

gen.getFoundersPAR

Internal function used by gen.findFounders

gen.nochildren

Number of children

geneaJi

Highly inbred pedigree

gen.pro

Get proband id numbers

gen.meangendepth

Expected Genealogical Depth

gen.rec

Ancestors coverage

gen.simuSample

Gene dropping simulations - Sample

gen.genout

Create pedigree data

gen.simuSampleFreq

Gene dropping simulations - Frequencies

gen.simuProb

Gene dropping simulations - Probabilities

gen.sibship

Get id numbers of siblings

gen.nomen

Number of men

gen.noind

Number of individuals

gen.nowomen

Number of women

pop140

Population of origin of the 140 Quebec samples

gen.phiCI

Average kinship confidence interval

gen.simuSet

Gene dropping simulations with specified transmission probabilities

gen.phiOver

Kinship above threshold

genea140

Genealogical information for 140 individuals from the Quebec Reference Sample

gen.climbPAR

Internal function used by gen.findMRCA