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:
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')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 7 months agofrom:84a2a9919f. Checks:OK: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 17 2024 |
| R-4.5-linux-x86_64 | OK | Sep 17 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 page | Topics |
|---|---|
| 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 subset | gen.branching |
| Get id numbers of children | gen.children |
| Internal function used by gen.findMRCA | gen.climbPAR |
| Completeness | gen.completeness |
| Variance of completeness index | gen.completenessVar |
| Genealogy depth | gen.depth |
| Inbreeding coefficient | gen.f |
| Average inbreeding coefficient confidence interval | gen.fCI |
| Finds the minimum distances between pairs of individuals given a set of ancestors. | gen.find.Min.Distance.MRCA |
| Minimum genetic distance between two individuals | gen.findDistance |
| Find common founder ancestors | gen.findFounders |
| Finding most recent common ancestors, MRCAs | gen.findMRCA |
| Get founder id numbers | gen.founder |
| Genetic contribution of ancestors | gen.gc |
| Create object of class GLgen | gen.genealogy |
| Create pedigree data | gen.genout |
| Internal function used by gen.findMRCA | gen.getAncestorsPAR |
| Internal function used by gen.findFounders | gen.getFoundersPAR |
| Pedigree graphical tool | gen.graph |
| Get half-founder id numbers | gen.half.founder |
| Genealogical implex | gen.implex |
| Variance of genealogical implex | gen.implexVar |
| Create object of class GLgen for maternal or paternal lineages | gen.lineages |
| Maximum number of generations | gen.max |
| Mean number of generations | gen.mean |
| Expected Genealogical Depth | gen.meangendepth |
| Variance of genealogical depth | gen.meangendepthVar |
| Minimum number of generations | gen.min |
| Number of children | gen.nochildren |
| Number of individuals | gen.noind |
| Number of men | gen.nomen |
| Number of women | gen.nowomen |
| Ancestor occurences | gen.occ |
| Get id numbers of parents | gen.parent |
| Kinship coefficient | gen.phi |
| Average kinship confidence interval | gen.phiCI |
| Average kinship | gen.phiMean |
| Kinship above threshold | gen.phiOver |
| Get proband id numbers | gen.pro |
| Ancestors coverage | gen.rec |
| Get id numbers of siblings | gen.sibship |
| Gene dropping simulations - haplotypes | gen.simuHaplo |
| Convert proband simulation results into sequence data given founder haplotypes | gen.simuHaplo_convert |
| Compare proband haplotypes for IBD sharing | gen.simuHaplo_IBD_compare |
| Trace inheritance path for results from gene dropping simulation | gen.simuHaplo_traceback |
| Gene dropping simulations - Probabilities | gen.simuProb |
| Gene dropping simulations - Sample | gen.simuSample |
| Gene dropping simulations - Frequencies | gen.simuSampleFreq |
| Gene dropping simulations with specified transmission probabilities | gen.simuSet |
| Genealogical information for 140 individuals from the Quebec Reference Sample | genea140 |
| Highly inbred pedigree | geneaJi |
| 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 samples | pop140 |