Package: GENLIB 1.1.10

Marie-Helene Roy-Gagnon

GENLIB: Genealogical Data Analysis

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>.

Authors:Louis Houde [aut], Jean-Francois Lefebvre [aut], Valery Roy-Lagace [aut], Sebastien Lemieux [aut], Michael J. Fromberger [ctb], Jarno van der Kolk [ctb], Mohan Rakesh [ctb], Marie-Helene Roy-Gagnon [cre]

GENLIB_1.1.10.tar.gz
GENLIB_1.1.10.tar.gz(r-4.5-noble)GENLIB_1.1.10.tar.gz(r-4.4-noble)
GENLIB_1.1.10.tgz(r-4.4-emscripten)GENLIB_1.1.10.tgz(r-4.3-emscripten)
GENLIB.pdf |GENLIB.html✨
GENLIB/json (API)

# Install 'GENLIB' in R:
install.packages('GENLIB', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • genea140 - Genealogical information for 140 individuals from the Quebec Reference Sample
  • geneaJi - Highly inbred pedigree
  • pop140 - Population of origin of the 140 Quebec samples

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

cpp

2.49 score 1 packages 51 scripts 317 downloads 2 mentions 49 exports 16 dependencies

Last updated 10 months agofrom:84a2a9919f. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 16 2024
R-4.5-linux-x86_64OKDec 16 2024

Exports:gen.branchinggen.childrengen.climbPARgen.completenessgen.completenessVargen.depthgen.fgen.fCIgen.find.Min.Distance.MRCAgen.findDistancegen.findFoundersgen.findMRCAgen.foundergen.gcgen.genealogygen.genoutgen.getAncestorsPARgen.getFoundersPARgen.graphgen.half.foundergen.implexgen.implexVargen.lineagesgen.maxgen.meangen.meangendepthgen.meangendepthVargen.mingen.nochildrengen.noindgen.nomengen.nowomengen.occgen.parentgen.phigen.phiCIgen.phiMeangen.phiOvergen.progen.recgen.sibshipgen.simuHaplogen.simuHaplo_convertgen.simuHaplo_IBD_comparegen.simuHaplo_tracebackgen.simuProbgen.simuSamplegen.simuSampleFreqgen.simuSet

Dependencies:BHbootstrapcodetoolsdoParallelevaluateforeachhighriteratorskinship2knitrlatticeMatrixquadprogRcppxfunyaml

Readme and manuals

Help Manual

Help pageTopics
Classes '"GLmultiVector"' '"GLmultiArray4"' '"GLmultiMatrix"' '"GLmultiNumber"'depth,GLmultiArray4-method depth,GLmultiMatrix-method depth,GLmultiNumber-method depth,GLmultiVector-method Dim,GLmultiArray4-method Dim,GLmultiMatrix-method Dim,GLmultiNumber-method Dim,GLmultiVector-method GLmultiArray4-class GLmultiMatrix-class GLmultiNumber-class GLmultiVector-class [,GLmultiArray4,ANY,ANY,ANY-method [,GLmultiMatrix,ANY,ANY,ANY-method [,GLmultiNumber,ANY,ANY,ANY-method [,GLmultiVector,ANY,ANY,ANY-method [<-,GLmultiArray4,ANY,ANY,ANY-method [<-,GLmultiMatrix,ANY,ANY,ANY-method [<-,GLmultiNumber,ANY,ANY,ANY-method [<-,GLmultiVector,ANY,ANY,ANY-method
Classes '"GLmultiPhiGroup"' '"GLmultiPhiGroupSingle"' '"GLmultiFGroup"' '"GLmultiFGroupSingle"' '"GLCGMatrixGroupSingle"'Dim,GLmultiFGroup-method Dim,GLmultiFGroupSingle-method Dim,GLmultiPhiGroup-method Dim,GLmultiPhiGroupSingle-method GLCGMatrixGroupSingle-class GLmultiFGroup-class GLmultiFGroupSingle-class GLmultiPhiGroup-class GLmultiPhiGroupSingle-class [,GLCGMatrixGroupSingle,ANY,ANY,ANY-method [,GLmultiFGroup,ANY,ANY,ANY-method [,GLmultiFGroupSingle,ANY,ANY,ANY-method [,GLmultiPhiGroup,ANY,ANY,ANY-method [,GLmultiPhiGroupSingle,ANY,ANY,ANY-method [<-,GLCGMatrixGroupSingle,ANY,ANY,ANY-method [<-,GLmultiFGroup,ANY,ANY,ANY-method [<-,GLmultiFGroupSingle,ANY,ANY,ANY-method [<-,GLmultiPhiGroup,ANY,ANY,ANY-method [<-,GLmultiPhiGroupSingle,ANY,ANY,ANY-method
Genealogy subsetgen.branching
Get id numbers of childrengen.children
Internal function used by gen.findMRCAgen.climbPAR
Completenessgen.completeness
Variance of completeness indexgen.completenessVar
Genealogy depthgen.depth
Inbreeding coefficientgen.f
Average inbreeding coefficient confidence intervalgen.fCI
Finds the minimum distances between pairs of individuals given a set of ancestors.gen.find.Min.Distance.MRCA
Minimum genetic distance between two individualsgen.findDistance
Find common founder ancestorsgen.findFounders
Finding most recent common ancestors, MRCAsgen.findMRCA
Get founder id numbersgen.founder
Genetic contribution of ancestorsgen.gc
Create object of class GLgengen.genealogy
Create pedigree datagen.genout
Internal function used by gen.findMRCAgen.getAncestorsPAR
Internal function used by gen.findFoundersgen.getFoundersPAR
Pedigree graphical toolgen.graph
Get half-founder id numbersgen.half.founder
Genealogical implexgen.implex
Variance of genealogical implexgen.implexVar
Create object of class GLgen for maternal or paternal lineagesgen.lineages
Maximum number of generationsgen.max
Mean number of generationsgen.mean
Expected Genealogical Depthgen.meangendepth
Variance of genealogical depthgen.meangendepthVar
Minimum number of generationsgen.min
Number of childrengen.nochildren
Number of individualsgen.noind
Number of mengen.nomen
Number of womengen.nowomen
Ancestor occurencesgen.occ
Get id numbers of parentsgen.parent
Kinship coefficientgen.phi
Average kinship confidence intervalgen.phiCI
Average kinshipgen.phiMean
Kinship above thresholdgen.phiOver
Get proband id numbersgen.pro
Ancestors coveragegen.rec
Get id numbers of siblingsgen.sibship
Gene dropping simulations - haplotypesgen.simuHaplo
Convert proband simulation results into sequence data given founder haplotypesgen.simuHaplo_convert
Compare proband haplotypes for IBD sharinggen.simuHaplo_IBD_compare
Trace inheritance path for results from gene dropping simulationgen.simuHaplo_traceback
Gene dropping simulations - Probabilitiesgen.simuProb
Gene dropping simulations - Samplegen.simuSample
Gene dropping simulations - Frequenciesgen.simuSampleFreq
Gene dropping simulations with specified transmission probabilitiesgen.simuSet
Genealogical information for 140 individuals from the Quebec Reference Samplegenea140
Highly inbred pedigreegeneaJi
Class '"GLgen"'depth,GLgen-method GLgen-class initialize,GLgen-method length,GLgen-method
Class '"GLgroup"'GLgroup-class initialize,GLgroup-method [,GLgroup,ANY,ANY,ANY-method
Class '"GLmultiList"'GLmultiList-class
Population of origin of the 140 Quebec samplespop140