Table 1 Overview of GENLIB functions
From: GENLIB: an R package for the analysis of genealogical data
Name | Use | |
|---|---|---|
Functions to manage genealogical objects | ||
gen.genalogy | To create a basic genealogical object | |
gen.lineages | To extract parental lineages from a genealogical object | |
gen.branching | To extract a subset of a genealogical object | |
gen.genout | To output a genealogical object as a data frame | |
gen.founder, gen.half.founder, gen.pro, gen.parent, gen.sibship, gen.children, gen.findFounders, gen.findMRCA | To identify specific individuals (founder, half-founder, proband, parent, sibship, children, common founder, most recent common ancestor) | |
Functions to describe… | ||
gen.nomen, gen.nowomen, gen.noind, gen.nochildren | …the number of men, women or individuals in a genealogy and number of kids an individual has | |
gen.min, gen.mean, gen.max | …the minimal, mean or maximal generation at which an individual can be found in a genealogy (first generation is coded 0) | |
gen.depth | …the number of generations in the genealogy | |
gen.completeness | …genealogical data completeness | |
gen.rec | …how many individuals within the specified individual group descend from each specified ancestor | |
gen.occ | …how many different (but not mutually exclusive) paths link an ancestor to a descendant | |
gen.meangendepth | …how much rooted are the genealogical lineages | |
gen.implex | …the extent of pedigree collapse within an individual’s genealogy | |
gen.findDistance | …distance between individuals through a specific ancestor | |
gen.find.Min.Distance.MRCA | …the shortest distances between individuals | |
Functions to plot… | ||
gen.graph | …the genealogy | |
Functions to compute … | ||
gen.phi | …the kinship matrix at specified generations | |
gen.f | …the inbreeding coefficients at specified generations | |
gen.gc | …the genetic contribution of ancestors to individuals | |
Gene-droppping simulation functions | ||
gen.simuProb | To compute the probability that individuals have 0, 1 or 2 copies of a disease allele knowing how many their ancestors had | |
gen.simuSample, gen.simuSampleFreq | To obtain the number (frequencies) of disease alleles for each individual taking into account each ancestor’s carrier status | |
gen.simuSet | As function gen.simuSample with option to customize transmission probabilities according to the parent’s and/or subject’s sex | |