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"' |