tidypopgen (version 0.4.3)

filter_high_relatedness: 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
)

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

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

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)