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GENLIB (version 1.0.4)

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

342

Version

1.0.4

License

GPL (>= 2)

Maintainer

Marie-Helene Roy-Gagnon

Last Published

April 21st, 2015

Functions in GENLIB (1.0.4)

gen.branching

Genealogy subset

gen.getAncestorsPAR

Internal function used by gen.findMRCA

gen.implex

Genealogical implex

gen.completenessVar

Variance of completeness index

gen.gc

Genetic contribution of ancestors

gen.findDistance

Minimum genetic distance between two individuals

gen.fCI

Average inbreeding coefficient confidence interval

gen.f

Inbreeding coefficient

gen.lineages

Create object of class GLgen for maternal or paternal lineages

GenlibR-package

Genealogical Data Analysis

gen.founder

Get founder id numbers

gen.meangendepth

Expected Genealogical Depth

gen.climbPAR

Internal function used by gen.findMRCA

Classes of basic handling of genealogy data

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

gen.genout

Create pedigree data

gen.findMRCA

Finding most recent common ancestors, MRCAs

gen.findFounders

Find common founder ancestors

gen.find.Min.Distance.MRCA

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

GLmultiList-class

Class "GLmultiList"

Internal function used by gen.findFounders

gen.genealogy

Create object of class GLgen

gen.meangendepthVar

Variance of genealogical depth

Classes of GLgroup handling

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

gen.completeness

Completeness

gen.graph

Pedigree graphical tool

gen.implexVar

Variance of genealogical implex

gen.children

Get id numbers of children

gen.half.founder

Get half-founder id numbers

GLgen-class

Class "GLgen"

geneaJi

Highly inbred pedigree

gen.nochildren

Number of children

gen.simuProb

Gene dropping simulations - Probabilities

pop140

Population of origin of the 140 Quebec samples

gen.mean

Mean number of generations

gen.occ

Ancestor occurences

gen.parent

Get id numbers of parents

gen.simuSet

Gene dropping simulations with specified transmission probabilities

gen.simuSample

Gene dropping simulations - Sample

genea140

Genealogical information for 140 individuals from the Quebec Reference Sample

gen.sibship

Get id numbers of siblings

Get proband id numbers

gen.noind

Number of individuals

gen.phiMean

Average kinship

gen.phiCI

Average kinship confidence interval

gen.simuSampleFreq

Gene dropping simulations - Frequencies

gen.rec

Ancestors coverage

gen.max

Maximum number of generations

gen.phiOver

Kinship above threshold

gen.nomen

Number of men

gen.min

Minimum number of generations