numberofalleles (version 1.0.1)

pr_independent_alleles_ped: Compute the probability distribution of the number of independent alleles in a mixture with dropout and related contributors

Description

When mixture contributors are related according to a pedigree, they may share some alleles identical by descent so that their total number of independent alleles is smaller than two times the number of contributors. The number of independent alleles can be further reduced if dropout plays a role. This function computes the probability distribution of the number of independent alleles that related mixture contributors have in total for a locus given their dropout parameters. Note that the number of distinct alleles that is observed at the locus is typically smaller than the number of independent alleles due to allele sharing.

Usage

pr_independent_alleles_ped(pedigree, ped_contributors, dropout_prs)

Arguments

pedigree

ped object

ped_contributors

Character vector with unique names of contributors. Valid names are the names of pedigree members.

dropout_prs

Numeric vector. Dropout probabilities per contributor.

Value

A named numeric vector describing the probability distribution. Numeric values are the probabilities corresponding to the names describing integer values.

See Also

pr_independent_alleles

Examples

# NOT RUN {
# without dropout, a father-mother-child mixture has 4 indep. alleles
p <- pr_independent_alleles_ped(pedtools::nuclearPed(),
                                ped_contributors = as.character(1:3),
                                dropout_prs = rep(0, 3))
stopifnot(identical(p,
                    stats::setNames(1., "4")))
# }