com2links: Convert Sparse Relationship Matrices to Kinship Links

In R-Computing-Lab/BGMisc: An R Package for Extended Behavior Genetics Analysis

Convert Sparse Relationship Matrices to Kinship Links

Description

This function processes one or more sparse relationship components (additive, mitochondrial, and common nuclear) and converts them into kinship link pairs. The resulting related pairs are either returned as a data frame or written to disk in CSV format.

Usage

com2links(
  rel_pairs_file = "dataRelatedPairs.csv",
  ad_ped_matrix = NULL,
  mit_ped_matrix = mt_ped_matrix,
  mt_ped_matrix = NULL,
  cn_ped_matrix = NULL,
  write_buffer_size = 1000,
  update_rate = 1000,
  gc = TRUE,
  writetodisk = TRUE,
  verbose = FALSE,
  legacy = FALSE,
  outcome_name = "data",
  drop_upper_triangular = TRUE,
  ...
)

Arguments

rel_pairs_file	File path to write related pairs to (CSV format).
ad_ped_matrix	Matrix of additive genetic relatedness coefficients.
mit_ped_matrix	Matrix of mitochondrial relatedness coefficients. Alias: mt_ped_matrix.
mt_ped_matrix	Matrix of mitochondrial relatedness coefficients.
cn_ped_matrix	Matrix of common nuclear relatedness coefficients.
write_buffer_size	Number of related pairs to write to disk at a time.
update_rate	Numeric. Frequency (in iterations) at which progress messages are printed.
gc	Logical. If TRUE, performs garbage collection via gc to free memory.
writetodisk	Logical. If TRUE, writes the related pairs to disk; if FALSE, returns a data frame.
verbose	Logical. If TRUE, prints progress messages.
legacy	Logical. If TRUE, uses the legacy branch of the function.
outcome_name	Character string representing the outcome name (used in file naming).
drop_upper_triangular	Logical. If TRUE, drops the upper triangular portion of the matrix.
...	Additional arguments to be passed to com2links

Value

A data frame of related pairs if writetodisk is FALSE; otherwise, writes the results to disk.

R-Computing-Lab/BGMisc documentation built on April 3, 2025, 3:12 p.m.