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GENLIB (version 1.0.6)

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

1.0.6

License

GPL (>= 2)

Maintainer

Marie-Helene Roy-Gagnon

Last Published

May 30th, 2018

Functions in GENLIB (1.0.6)

gen.founder

Get founder id numbers

gen.f

Inbreeding coefficient

Classes of basic handling of genealogy data

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

gen.meangendepthVar

Variance of genealogical depth

gen.gc

Genetic contribution of ancestors

GenlibR-package

Genealogical Data Analysis

gen.findMRCA

Finding most recent common ancestors, MRCAs

gen.min

Minimum number of generations

gen.phiOver

Kinship above threshold

gen.phiMean

Average kinship

gen.genealogy

Create object of class GLgen

gen.findFounders

Find common founder ancestors

gen.fCI

Average inbreeding coefficient confidence interval

geneaJi

Highly inbred pedigree

gen.genout

Create pedigree data

pop140

Population of origin of the 140 Quebec samples

gen.completenessVar

Variance of completeness index

gen.getAncestorsPAR

Internal function used by gen.findMRCA

gen.graph

Pedigree graphical tool

gen.depth

Genealogy depth

gen.getFoundersPAR

Internal function used by gen.findFounders

gen.half.founder

Get half-founder id numbers

gen.lineages

Create object of class GLgen for maternal or paternal lineages

gen.simuSet

Gene dropping simulations with specified transmission probabilities

gen.implex

Genealogical implex

gen.implexVar

Variance of genealogical implex

Genealogical information for 140 individuals from the Quebec Reference Sample

Number of individuals

gen.max

Maximum number of generations

gen.phiCI

Average kinship confidence interval

gen.sibship

Get id numbers of siblings

gen.mean

Mean number of generations

gen.simuProb

Gene dropping simulations - Probabilities

gen.occ

Ancestor occurences

gen.meangendepth

Expected Genealogical Depth

gen.parent

Get id numbers of parents

gen.simuSample

Gene dropping simulations - Sample

gen.simuSampleFreq

Gene dropping simulations - Frequencies

gen.pro

Get proband id numbers

gen.rec

Ancestors coverage

GLmultiList-class

Class "GLmultiList"

gen.children

Get id numbers of children

gen.branching

Genealogy subset

gen.climbPAR

Internal function used by gen.findMRCA

Classes of GLgroup handling

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

gen.findDistance

Minimum genetic distance between two individuals

gen.find.Min.Distance.MRCA

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

GLgen-class

Class "GLgen"