GENLIB: Genealogical Data Analysis

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

Author
Louis Houde [aut], Jean-Francois Lefebvre [aut], Valery Roy-Lagace [aut], Sebastien Lemieux [aut], Michael J. Fromberger [ctb], Marie-Helene Roy-Gagnon [cre]
Date of publication
2015-04-21 07:54:37
Maintainer
Marie-Helene Roy-Gagnon <mroygagn@uottawa.ca>
License
GPL (>= 2)
Version
1.0.4

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