GENLIB1.1.10 package

Genealogical Data Analysis

gen.branching

Genealogy subset

gen.children

Get id numbers of children

gen.climbPAR

Internal function used by gen.findMRCA

gen.completeness

Completeness

gen.completenessVar

Variance of completeness index

gen.depth

Genealogy depth

gen.f

Inbreeding coefficient

gen.fCI

Average inbreeding coefficient confidence interval

gen.find.Min.Distance.MRCA

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

gen.findDistance

Minimum genetic distance between two individuals

gen.findFounders

Find common founder ancestors

gen.findMRCA

Finding most recent common ancestors, MRCAs

gen.founder

Get founder id numbers

gen.gc

Genetic contribution of ancestors

gen.genealogy

Create object of class GLgen

gen.genout

Create pedigree data

gen.getAncestorsPAR

Internal function used by gen.findMRCA

gen.getFoundersPAR

Internal function used by gen.findFounders

gen.graph

Pedigree graphical tool

gen.half.founder

Get half-founder id numbers

gen.implex

Genealogical implex

gen.implexVar

Variance of genealogical implex

gen.lineages

Create object of class GLgen for maternal or paternal lineages

gen.max

Maximum number of generations

gen.mean

Mean number of generations

gen.meangendepth

Expected Genealogical Depth

gen.meangendepthVar

Variance of genealogical depth

gen.min

Minimum number of generations

gen.nochildren

Number of children

gen.noind

Number of individuals

gen.nomen

Number of men

gen.nowomen

Number of women

gen.occ

Ancestor occurences

gen.parent

Get id numbers of parents

gen.phi

Kinship coefficient

gen.phiCI

Average kinship confidence interval

gen.phiMean

Average kinship

gen.phiOver

Kinship above threshold

gen.pro

Get proband id numbers

gen.rec

Ancestors coverage

gen.sibship

Get id numbers of siblings

gen.simuHaplo

Gene dropping simulations - haplotypes

gen.simuHaplo_convert

Convert proband simulation results into sequence data given founder ha...

gen.simuHaplo_IBD_compare

Compare proband haplotypes for IBD sharing

gen.simuHaplo_traceback

Trace inheritance path for results from gene dropping simulation

gen.simuProb

Gene dropping simulations - Probabilities

gen.simuSample

Gene dropping simulations - Sample

gen.simuSampleFreq

Gene dropping simulations - Frequencies

gen.simuSet

Gene dropping simulations with specified transmission probabilities

GLCGMatrixGroupSingle-class

Classes "GLmultiPhiGroup" "GLmultiPhiGroupSingle" `"GLmultiFGroup"...

GLgen-class

Class "GLgen"

GLgroupe-class

Class "GLgroup"

GLmultiList-class

Class "GLmultiList"

GLmultiVector-class

Classes "GLmultiVector" "GLmultiArray4" "GLmultiMatrix" `"GLmult...

Genealogical data analysis including descriptive statistics (e.g., kinship and inbreeding coefficients) and gene-dropping simulations. See: "GENLIB: an R package for the analysis of genealogical data" Gauvin et al. (2015) <doi:10.1186/s12859-015-0581-5>.

  • Maintainer: Marie-Helene Roy-Gagnon
  • License: GPL (>= 2)
  • Last published: 2024-02-19