GENLIB: Genealogical Data Analysis

Genealogical data analysis including descriptive statistics (e.g., kinship and inbreeding coefficients) and gene-dropping simulations.

AuthorLouis Houde [aut], Jean-Francois Lefebvre [aut], Valery Roy-Lagace [aut], Sebastien Lemieux [aut], Michael J. Fromberger [ctb], Marie-Helene Roy-Gagnon [cre]
Date of publication2015-04-21 07:54:37
MaintainerMarie-Helene Roy-Gagnon <mroygagn@uottawa.ca>
LicenseGPL (>= 2)
Version1.0.4

View on CRAN

Man pages

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

genea140: Genealogical information for 140 individuals from the Quebec...

geneaJi: Highly inbred pedigree

gen.f: Inbreeding coefficient

gen.fCI: Average inbreeding coefficient confidence interval

gen.findDistance: Minimum genetic distance between two individuals

gen.findFounders: Find common founder ancestors

gen.find.Min.Distance.MRCA: Finds the minimum distances between pairs of individuals...

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

GenlibR-package: Genealogical Data Analysis

gen.lineages: Create object of class GLgen for maternal or paternal...

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.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...

GLCGMatrixGroupSingle-class: Classes '"GLmultiPhiGroup"' '"GLmultiPhiGroupSingle"'...

GLgen-class: Class '"GLgen"'

GLgroupe-class: Class '"GLgroup"'

GLmultiList-class: Class '"GLmultiList"'

GLmultiVector-class: Classes '"GLmultiVector"' '"GLmultiArray4"' '"GLmultiMatrix"'...

pop140: Population of origin of the 140 Quebec samples

Files in this package

GENLIB
GENLIB/src
GENLIB/src/hashtable.h
GENLIB/src/genlibDLL.h
GENLIB/src/Makevars
GENLIB/src/apparentement.cpp
GENLIB/src/statanal.cpp
GENLIB/src/statanal.h
GENLIB/src/probsimul.h
GENLIB/src/genphi.h
GENLIB/src/genphi.cpp
GENLIB/src/outilsalloc.h
GENLIB/src/fondateur.h
GENLIB/src/base.h
GENLIB/src/apparentement.h
GENLIB/src/mpi.h
GENLIB/src/logtab.h
GENLIB/src/mpajout.c
GENLIB/src/exception.h
GENLIB/src/mpi-types.h
GENLIB/src/mpi-config.h
GENLIB/src/mplogic.h
GENLIB/src/mpi.c
GENLIB/src/consanguinite.h
GENLIB/src/outils.cpp
GENLIB/src/userInterface.h
GENLIB/src/hal.cpp
GENLIB/src/interface.h
GENLIB/src/outilanal.h
GENLIB/src/consanguinite.cpp
GENLIB/src/congen.h
GENLIB/src/mplogic.c
GENLIB/src/md5.cpp
GENLIB/src/congen.cpp
GENLIB/src/hal.h
GENLIB/src/fondateur.cpp
GENLIB/src/cbignum.h
GENLIB/src/outils.h
GENLIB/src/probsimul.cpp
GENLIB/src/Makevars.win
GENLIB/src/interface.cpp
GENLIB/src/userInterface.cpp
GENLIB/src/md5.h
GENLIB/src/outilanal.cpp
GENLIB/src/basemt.h
GENLIB/src/exception.cpp
GENLIB/NAMESPACE
GENLIB/data
GENLIB/data/genea140.rda
GENLIB/data/pop140.rda
GENLIB/data/geneaJi.rda
GENLIB/R
GENLIB/R/classes_methodes.R GENLIB/R/fonctionsSimul.R GENLIB/R/genlibDLL.R GENLIB/R/fonctionsBase.R GENLIB/R/fonctionsPAR.R GENLIB/R/fonctionsPriv.R GENLIB/R/fonctionsGraph.R GENLIB/R/fonctionsStat.R
GENLIB/MD5
GENLIB/DESCRIPTION
GENLIB/man
GENLIB/man/pop140.Rd GENLIB/man/gen.branching.Rd GENLIB/man/gen.getFoundersPAR.Rd GENLIB/man/gen.fCI.Rd GENLIB/man/gen.founder.Rd GENLIB/man/gen.phiOver.Rd GENLIB/man/gen.find.Min.Distance.MRCA.Rd GENLIB/man/GLmultiList-class.Rd GENLIB/man/gen.implexVar.Rd GENLIB/man/gen.nowomen.Rd GENLIB/man/gen.meangendepth.Rd GENLIB/man/gen.simuSampleFreq.Rd GENLIB/man/gen.mean.Rd GENLIB/man/GLCGMatrixGroupSingle-class.Rd GENLIB/man/gen.findDistance.Rd GENLIB/man/gen.genout.Rd GENLIB/man/gen.noind.Rd GENLIB/man/gen.genealogy.Rd GENLIB/man/gen.meangendepthVar.Rd GENLIB/man/gen.occ.Rd GENLIB/man/gen.simuProb.Rd GENLIB/man/gen.simuSet.Rd GENLIB/man/GenlibR-package.Rd GENLIB/man/gen.completenessVar.Rd GENLIB/man/gen.half.founder.Rd GENLIB/man/geneaJi.Rd GENLIB/man/gen.f.Rd GENLIB/man/gen.climbPAR.Rd GENLIB/man/GLgen-class.Rd GENLIB/man/gen.max.Rd GENLIB/man/genea140.Rd GENLIB/man/gen.findFounders.Rd GENLIB/man/gen.rec.Rd GENLIB/man/gen.parent.Rd GENLIB/man/gen.implex.Rd GENLIB/man/gen.completeness.Rd GENLIB/man/gen.depth.Rd GENLIB/man/gen.phiCI.Rd GENLIB/man/gen.graph.Rd GENLIB/man/gen.phi.Rd GENLIB/man/gen.sibship.Rd GENLIB/man/gen.findMRCA.Rd GENLIB/man/gen.lineages.Rd GENLIB/man/gen.nomen.Rd GENLIB/man/gen.getAncestorsPAR.Rd GENLIB/man/gen.children.Rd GENLIB/man/gen.nochildren.Rd GENLIB/man/gen.gc.Rd GENLIB/man/GLmultiVector-class.Rd GENLIB/man/gen.min.Rd GENLIB/man/gen.simuSample.Rd GENLIB/man/gen.phiMean.Rd GENLIB/man/GLgroupe-class.Rd GENLIB/man/gen.pro.Rd

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