FamiliasPrior: Calculates a prior distribution for a list of pedigrees

In Familias: Probabilities for Pedigrees Given DNA Data

Calculates a prior distribution for a list of pedigrees

Description

By default the same prior probability is assigned to all pedigrees in the list, but this can be adjusted with the function parameters. It is computed which persons are common to all the pedigrees listed, and they are handled in a special way: It is with relation to these persons that the number of generations and other parameters are computed. Also, the function will search for and remove pedigrees that are "equivalent" in terms of representing the relationship between these core persons. So if another pedigree is added, with all new persons, the function will return with an error message.

Usage

FamiliasPrior(pedigrees, 
              generationsParameter = 1, 
              inbreedingParameter = 1, 
              partnerParameter = 1, 
              maxGenerations)

Arguments

pedigrees	A list of objects of class either 'pedigree' or 'FamiliasPedigree'.
generationsParameter	Non-negative real. A value of 1 indicates no influence of the parameter. A value above 1 (below 1) increases (decreases) the prior probability for pedigrees with many generations.
inbreedingParameter	Non-negative real. A pedigree is inbred if parents are related within the pedigree. If 0, all inbred pedigrees are assigned a prior probability 0. A value of 1 indicates no influence of inbreeding. A value above 1 (below 1) increases (decreases) the prior for inbred pedigrees.
partnerParameter	Non-negative real (previously referred to as promiscuity parameter). If 0, all pedigrees where parents have children by different partners, are assigned prior 0. A value of 1 indicates no influence of the parameter. A value above 1 (below 1) increases (decreases) the prior for partners having children by different partners.
maxGenerations	Integer giving the maximum number of generations; pedigrees with more generations than this are assigned a zero prior probability.

Details

See https://familias.name/manual.pdf for a complete description of the parametric models implemented.

Value

The prior, i.e., a vector of real numbers summing to 1.

Author(s)

Petter Mostad <[e-mail]> and Thore Egeland <[e-mail]>

Examples

persons <- c("mother", "daughter", "AF")
ped1 <- FamiliasPedigree(id = persons, 
                         dadid = c(NA, "AF", NA), 
                         momid = c(NA, "mother", NA),
                         sex = c("female", "female", "male"))
ped2 <- FamiliasPedigree(id = c(persons, "TF"), 
                         dadid = c(NA, "TF", NA, NA), 
                         momid = c(NA, "mother", NA, NA), 
                         sex = c("female", "female", "male", "male"))
ped3 <- FamiliasPedigree(id = c(persons, "TF", "gf", "gm"), 
                         dadid = c(NA, "TF", "gf", "gf", NA, NA), 
                         momid = c(NA, "mother", "gm", "gm", NA, NA), 
                         sex = c("female", "female", "male", "male", "male", "female"))
                         
mypedigrees <- list(isFather = ped1, unrelated = ped2, isUncle = ped3)

FamiliasPrior(mypedigrees)

granddad <- FamiliasPedigree(id = c(persons, "TF", "gm"), 
                             dadid = c(NA, "TF", NA, "AF", NA),
                             momid = c(NA, "mother", NA, "gm", NA), 
                             sex = c("female", "female", "male", "male", "female"))
FamiliasPrior(c(mypedigrees, list(granddad)))
FamiliasPrior(c(mypedigrees, list(granddad)), maxGenerations = 1)

Familias documentation built on May 29, 2024, 10:49 a.m.