Genealogical Data Analysis
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Documentation for package ‘GENLIB’ version 1.1.10
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| depth-method | Class '"GLgen"' |
| depth-method | Classes '"GLmultiVector"' '"GLmultiArray4"' '"GLmultiMatrix"' '"GLmultiNumber"' |
| Dim-method | Classes '"GLmultiPhiGroup"' '"GLmultiPhiGroupSingle"' '"GLmultiFGroup"' '"GLmultiFGroupSingle"' '"GLCGMatrixGroupSingle"' |
| Dim-method | Classes '"GLmultiVector"' '"GLmultiArray4"' '"GLmultiMatrix"' '"GLmultiNumber"' |
| 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 |
| gen.f | Inbreeding coefficient |
| gen.fCI | Average inbreeding coefficient confidence interval |
| gen.find.Min.Distance.MRCA | Finds the minimum distances between pairs of individuals given a set of ancestors. |
| gen.findDistance | Minimum genetic distance between two individuals |
| gen.findFounders | Find common founder ancestors |
| 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 |
| gen.lineages | Create object of class GLgen for maternal or paternal lineages |
| 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.simuHaplo | Gene dropping simulations - haplotypes |
| gen.simuHaplo_convert | Convert proband simulation results into sequence data given founder haplotypes |
| gen.simuHaplo_IBD_compare | Compare proband haplotypes for IBD sharing |
| gen.simuHaplo_traceback | Trace inheritance path for results from gene dropping simulation |
| 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 probabilities |
| genea140 | Genealogical information for 140 individuals from the Quebec Reference Sample |
| geneaJi | Highly inbred pedigree |
| GLCGMatrixGroupSingle-class | Classes '"GLmultiPhiGroup"' '"GLmultiPhiGroupSingle"' '"GLmultiFGroup"' '"GLmultiFGroupSingle"' '"GLCGMatrixGroupSingle"' |
| GLgen-class | Class '"GLgen"' |
| GLgroup-class | Class '"GLgroup"' |
| GLmultiArray4-class | Classes '"GLmultiVector"' '"GLmultiArray4"' '"GLmultiMatrix"' '"GLmultiNumber"' |
| GLmultiFGroup-class | Classes '"GLmultiPhiGroup"' '"GLmultiPhiGroupSingle"' '"GLmultiFGroup"' '"GLmultiFGroupSingle"' '"GLCGMatrixGroupSingle"' |
| GLmultiFGroupSingle-class | Classes '"GLmultiPhiGroup"' '"GLmultiPhiGroupSingle"' '"GLmultiFGroup"' '"GLmultiFGroupSingle"' '"GLCGMatrixGroupSingle"' |
| GLmultiList-class | Class '"GLmultiList"' |
| GLmultiMatrix-class | Classes '"GLmultiVector"' '"GLmultiArray4"' '"GLmultiMatrix"' '"GLmultiNumber"' |
| GLmultiNumber-class | Classes '"GLmultiVector"' '"GLmultiArray4"' '"GLmultiMatrix"' '"GLmultiNumber"' |
| GLmultiPhiGroup-class | Classes '"GLmultiPhiGroup"' '"GLmultiPhiGroupSingle"' '"GLmultiFGroup"' '"GLmultiFGroupSingle"' '"GLCGMatrixGroupSingle"' |
| GLmultiPhiGroupSingle-class | Classes '"GLmultiPhiGroup"' '"GLmultiPhiGroupSingle"' '"GLmultiFGroup"' '"GLmultiFGroupSingle"' '"GLCGMatrixGroupSingle"' |
| GLmultiVector-class | Classes '"GLmultiVector"' '"GLmultiArray4"' '"GLmultiMatrix"' '"GLmultiNumber"' |
| initialize-method | Class '"GLgen"' |
| initialize-method | Class '"GLgroup"' |
| length-method | Class '"GLgen"' |
| pop140 | Population of origin of the 140 Quebec samples |
| [-method | Classes '"GLmultiPhiGroup"' '"GLmultiPhiGroupSingle"' '"GLmultiFGroup"' '"GLmultiFGroupSingle"' '"GLCGMatrixGroupSingle"' |
| [-method | Class '"GLgroup"' |
| [-method | Classes '"GLmultiVector"' '"GLmultiArray4"' '"GLmultiMatrix"' '"GLmultiNumber"' |
| [<--method | Classes '"GLmultiPhiGroup"' '"GLmultiPhiGroupSingle"' '"GLmultiFGroup"' '"GLmultiFGroupSingle"' '"GLCGMatrixGroupSingle"' |
| [<--method | Classes '"GLmultiVector"' '"GLmultiArray4"' '"GLmultiMatrix"' '"GLmultiNumber"' |