descent: Multigene Descent Probabilities

In sped: Multi-Gene Descent Probabilities

Multigene Descent Probabilities

Description

Calculate probabilities that genes randomly chosen from some set of individuals are descended from some specified set of genes.

Usage

descent(individuals, pedigree, geneset, check.sex=FALSE)

Arguments

individuals	an atomic vector of names of individuals. Must be of type integer or character.
pedigree	a matrix with three columns. Each row contains the name of an individual and its father and mother, in that order. Must be the same type as the preceding argument.
geneset	an integer vector having names that are contained in the preceding argument. Allowed values are 0, 1, or 2, but zero values may be omitted.
check.sex	If TRUE check that no individual appears in both the father column and the mother column of argument pedigree.

Details

We work relative to the pedigree defined by argument pedigree in which every individual has either two parents or none specified. Those with none specified are called founders. Any ancestors of founders are assumed to not be individuals in the pedigree, that is, we are assuming all unknown individuals are different from all known individuals.

Thompson (1983) defines multigene descent probabilities g_S(B_1, \ldots, B_n) to be the probability that genes at one autosomal locus randomly chosen from each of the individuals B_1, ..., B_n are all descended from genes (not necessarily the same gene) in some set S of genes in individuals in the pedigree. The individuals need not be distinct (there can be repeats). The individuals are specified by argument individuals. The gene set S is specified by argument geneset.

Value

the calculated probability.

References

Geyer, C.~J. (1988) Software for calculating gene survival and multigene descent probabilities and for pedigree manipulation and drawing. Technical Report No. 153, Department of Statistics, University of Washington. https://stat.uw.edu/sites/default/files/files/reports/1988/tr153.pdf.

Thompson, E. A. (1983) Gene extinction and allelic origins in complex genealogies (with discussion). Proceedings of the Royal Society of London. Series B, Biological Sciences, 219, 241–251. \Sexpr[results=rd]{tools:::Rd_expr_doi("doi:10.1098/rspb.1983.0072")}.

Thompson, E. A. (1986) Ancestry of alleles and extinction of genes in populations with defined pedigrees. Zoo Biology, 5, 161–170. \Sexpr[results=rd]{tools:::Rd_expr_doi("doi:10.1002/zoo.1430050210")}.

Examples

# In alberta pedigree, probability that one gene picked at random
# from individual 1260 is descended from one gene in founder 52.
library(sped)
data(alberta)

descent(1260, alberta, c("52"=1))

sped documentation built on July 26, 2023, 5:13 p.m.