Special {sped} | R Documentation |
Special Multigene Descent Probabilities
Description
Calculate particular multigene descent probabilities of particular interest.
Usage
alphas(individuals, pedigree)
betas(individuals, pedigree)
gammas(individuals, pedigree)
inbreeding(individuals, pedigree)
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. |
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.
Value
A matrix whose rows are probabilities relating to particular founders and whose columns are probabilities relating to particular individuals. The row and column labels say which founders and which individuals.
R function gammas
gives the probability that a gene chosen at random
from the individual comes from either gene of the founder.
R function betas
gives the probability that both genes
from the individual comes from the genes (not necessarily the same gene)
of the founder.
R function alphas
gives inbreeding of the individual relative
to the founder: the probability that both genes
from the individual comes from the same gene (either gene) of the founder.
R function inbreeding
gives inbreeding coefficients of the individuals.
R function kinship
returns a matrix whose entries are the kinship
coefficients of the individuals.
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. 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. doi:10.1002/zoo.1430050210.
See Also
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)
gammas(c(1260, 1272), alberta)
data(thompson)
betas(c("U", "V", "Q", "R", "W"), thompson)
alphas(c("U", "V", "Q", "R", "W"), thompson)
inbreeding(c("U", "V", "Q", "R", "W"), thompson)
kinship(c("U", "V", "Q", "R", "W"), thompson)