find_ancestors_and_relatives_of_samples: Find ancestors and relative of each sampled member of a...

In CKMRpop: Forward-in-Time Simulation and Tallying of Pairwise Relationships

Description

This is a fairly general function that can be applied to pedigree output from any simulation program. It calls a function written in C++ to do all the recursive pedigree searching.

Usage

find_ancestors_and_relatives_of_samples(P, S, n)

Arguments

P	a tibble that gives the pedigree. It must have the columns kid, pa, ma. These columns must be character vectors of the unique IDs for each individual in the pedigree. Every individual in the pedigree must appear exactly once in the kid column. When founders appear in the pedigree, their pa and ma entries must be "0" (i.e. character zero).
S	a vector of the IDs of the sampled individuals. Obviously, all members of S must appear in P.
n	number of generations back from the sampled individuals to return in each individual's ancestor vector. 0 = self, 1 = back to and including the parents, 2 = back to and including the grandparents, and so on.

Value

A tibble with three columns:

• sample_id: the ID names of the sampled individuals

• ancestors: a list column. Each element is a vector of the ids of the ancestors of the sampled individual in the 2^(n+1) - 1 positions. The first is the sampled individual, the second is pa, third is ma, fourth is pa's pa, fifth is pa's ma, sixth is ma's pa, and so forth.

• relatives: a list column. Each element is a vector of the ids of the individuals that are sampled relatives within the n generations. The first element is the sampled individual itself, and the remaining ones are all the relatives of that individual whom were also sampled.

Examples

# get some input variables
P <- three_pops_with_mig_slurped_results$pedigree
S <- three_pops_with_mig_slurped_results$samples$ID
n <- 2
result <- find_ancestors_and_relatives_of_samples(P, S, n)
result

CKMRpop documentation built on July 17, 2021, 5:07 p.m.