filter_high_relatedness: Filter individuals based on a relationship threshold

In tidypopgen: Tidy Population Genetics

Filter individuals based on a relationship threshold

Description

This function takes a matrix of x by y individuals containing relatedness coefficients and returns the maximum set of individuals that contains no relationships above the given threshold.

Usage

filter_high_relatedness(
  matrix,
  .x = NULL,
  kings_threshold = NULL,
  verbose = FALSE
)

Arguments

matrix	a square symmetric matrix of individuals containing relationship coefficients
.x	a gen_tibble object
kings_threshold	a threshold over which
verbose	boolean whether to report to screen

Value

a list where '1' is individual ID's to retain, '2' is individual ID's to remove, and '3' is a boolean where individuals to keep are TRUE and individuals to remove are FALSE

Examples

example_gt <- load_example_gt("gen_tbl")

# Calculate relationship matrix
king_matrix <- example_gt %>% pairwise_king(as_matrix = TRUE)

# Filter individuals with threshold above 0.2
filter_high_relatedness(king_matrix, example_gt, kings_threshold = 0.2)

tidypopgen documentation built on Aug. 28, 2025, 1:08 a.m.