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

Functions

depth,GLgen-method Man page
depth,GLmultiArray4-method Man page
depth,GLmultiMatrix-method Man page
depth,GLmultiNumber-method Man page
depth,GLmultiVector-method Man page
Dim,GLmultiArray4-method Man page
Dim,GLmultiFGroup-method Man page
Dim,GLmultiFGroupSingle-method Man page
Dim,GLmultiMatrix-method Man page
Dim,GLmultiNumber-method Man page
Dim,GLmultiPhiGroup-method Man page
Dim,GLmultiPhiGroupSingle-method Man page
Dim,GLmultiVector-method Man page
gen.branching Man page
gen.children Man page
gen.climbPAR Man page
gen.completeness Man page
gen.completenessVar Man page
gen.depth Man page
genea140 Man page
geneaJi Man page
gen.f Man page
gen.fCI Man page
gen.findDistance Man page
gen.findFounders Man page
gen.find.Min.Distance.MRCA Man page
gen.findMRCA Man page
gen.founder Man page
gen.gc Man page
gen.genealogy Man page
gen.genout Man page
gen.getAncestorsPAR Man page
gen.getFoundersPAR Man page
gen.graph Man page
gen.half.founder Man page
gen.implex Man page
gen.implexVar Man page
GenlibR-package Man page
gen.lineages Man page
gen.max Man page
gen.mean Man page
gen.meangendepth Man page
gen.meangendepthVar Man page
gen.min Man page
gen.nochildren Man page
gen.noind Man page
gen.nomen Man page
gen.nowomen Man page
gen.occ Man page
gen.parent Man page
gen.phi Man page
gen.phiCI Man page
gen.phiMean Man page
gen.phiOver Man page
gen.pro Man page
gen.rec Man page
gen.sibship Man page
gen.simuProb Man page
gen.simuSample Man page
gen.simuSampleFreq Man page
gen.simuSet Man page
[<-,GLCGMatrixGroupSingle,ANY,ANY,ANY-method Man page
[,GLCGMatrixGroupSingle,ANY,ANY,ANY-method Man page
GLCGMatrixGroupSingle-class Man page
GLgen-class Man page
[,GLgroup,ANY,ANY,ANY-method Man page
GLgroup-class Man page
[<-,GLmultiArray4,ANY,ANY,ANY-method Man page
[,GLmultiArray4,ANY,ANY,ANY-method Man page
GLmultiArray4-class Man page
[<-,GLmultiFGroup,ANY,ANY,ANY-method Man page
[,GLmultiFGroup,ANY,ANY,ANY-method Man page
GLmultiFGroup-class Man page
[<-,GLmultiFGroupSingle,ANY,ANY,ANY-method Man page
[,GLmultiFGroupSingle,ANY,ANY,ANY-method Man page
GLmultiFGroupSingle-class Man page
GLmultiList-class Man page
[<-,GLmultiMatrix,ANY,ANY,ANY-method Man page
[,GLmultiMatrix,ANY,ANY,ANY-method Man page
GLmultiMatrix-class Man page
[<-,GLmultiNumber,ANY,ANY,ANY-method Man page
[,GLmultiNumber,ANY,ANY,ANY-method Man page
GLmultiNumber-class Man page
[<-,GLmultiPhiGroup,ANY,ANY,ANY-method Man page
[,GLmultiPhiGroup,ANY,ANY,ANY-method Man page
GLmultiPhiGroup-class Man page
[<-,GLmultiPhiGroupSingle,ANY,ANY,ANY-method Man page
[,GLmultiPhiGroupSingle,ANY,ANY,ANY-method Man page
GLmultiPhiGroupSingle-class Man page
[<-,GLmultiVector,ANY,ANY,ANY-method Man page
[,GLmultiVector,ANY,ANY,ANY-method Man page
GLmultiVector-class Man page
initialize,GLgen-method Man page
initialize,GLgroup-method Man page
length,GLgen-method Man page
pop140 Man page

Files

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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