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GENLIB (version 1.0.1)

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

1.0.1

License

GPL (>= 2)

Maintainer

Marie-Helene Roy-Gagnon

Last Published

September 26th, 2014

Functions in GENLIB (1.0.1)

gen.completeness

Completeness

Classes of GLgroupe handling

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

GLmultiList-class

Class "GLmultiList"

gen.f

Inbreeding coefficient

gen.completenessVar

Variance of completeness index

gen.find.Min.Distance.MRCA

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

Classes of basic handling of genealogy data

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

gen.children

Get id numbers of children

gen.getAncestorsPAR

Internal function used by gen.findMRCA

gen.findFounders

Find common founder ancestors

gen.half.founder

Get half-founder id numbers

GLgen-class

Class "GLgen"

gen.gc

Genetci contribution of ancestors

gen.implexVar

Variance of genealogical implex

gen.max

Maximum number of generations

gen.fCI

Average inbreeding coefficient confidence interval

gen.founder

Get founder id numbers

gen.branching

Genealogy subset

GenlibR-package

Genealogical Data Analysis

GLgroupe-class

Class "GLgroupe"

gen.entropyVar

Variance of entropy index

gen.genealogy

Create object of class GLgen

gen.lineages

Create object of class GLgen for maternal or paternal lineages

gen.entropy

Genelogical entropy (expected genealogical depth)

gen.graph

Pedigree graphical tool

Internal function used by gen.findMRCA

gen.getFoundersPAR

Internal function used by gen.findFounders

gen.rec

Ancestors coverage

gen.simuSet

Gene dropping simulations with specified transmission probabilities

gen.simuSampleFreq

Gene dropping simulations - Frequencies

gen.nomen

Number of men

gen.phiOver

Kinship above threshold

gen.parent

Get id numbers of parents

Genealogical information for 140 individuals from the Quebec Reference Sample

gen.phiCI

Average kinship confidence interval

gen.mean

Mean number of generations

gen.min

Minimum number of generations

gen.noind

Number of individuals

gen.phiMean

Average kinship

gen.sibship

Get id numbers of siblings

gen.occ

Ancestor occurences

gen.simuSample

Gene dropping simulations - Sample

gen.pro

Get proband id numbers

geneaJi

Highly inbred pedigree

gen.phi

Kinship coefficient

gen.findMRCA

Finding most recent common ancestors, MRCAs

gen.findDistance

Minimum genetic distance between two individuals

gen.nowomen

Number of women

pop140

Population of origin of the 140 Quebec samples

gen.simuProb

Gene dropping simulations - Probabilities

gen.meangendepthVar

Variance of genealogical depth

gen.climbPAR

Internal function used by gen.findMRCA

GLgroup-class

Class "GLgroup"

Classes of GLgroup handling

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

gen.meangendepth

Expected Genealogical Depth