sliceFamilies: sliceFamilies

In BGmisc: An R Package for Extended Behavior Genetics Analysis

sliceFamilies

Description

Slices up families by additive relatedness, creating CSV files grouped by degree of relatedness. Operates on a potentially large file by reading in chunks and binning links by additive relatedness.

Usage

sliceFamilies(
  outcome_name = "AD_demo",
  biggest = TRUE,
  bin_width = 0.1,
  degreerelatedness = 12,
  chunk_size = 2e+07,
  max_lines = 1e+13,
  addRel_ceiling = 1.5,
  input_file = NULL,
  folder_prefix = "data",
  progress_csv = "progress.csv",
  progress_status = "progress.txt",
  data_directory = NULL,
  verbose = FALSE,
  error_handling = FALSE,
  file_column_names = c("ID1", "ID2", "addRel", "mitRel", "cnuRel")
)

Arguments

outcome_name	Name of the outcome variable (used for naming input/output files)
biggest	Logical; whether to process the "biggest" family dataset (TRUE) or all-but-biggest (FALSE)
bin_width	Width of additive relatedness bins (default is 0.10)
degreerelatedness	Maximum degree of relatedness to consider (default 12)
chunk_size	Number of lines to read in each chunk (default 2e7)
max_lines	Max number of lines to process from input file (default 1e13)
addRel_ceiling	Numeric. Maximum relatedness value to bin to. Default is 1.5
input_file	Path to the input CSV file. If NULL, defaults to a specific file based on 'biggest' flag.
folder_prefix	Prefix for the output folder (default "data")
progress_csv	Path to a CSV file for tracking progress (default "progress.csv")
progress_status	Path to a text file for logging progress status (default "progress.txt")
data_directory	Directory where output files will be saved. If NULL, it is constructed based on 'outcome_name' and 'folder_prefix'.
verbose	Logical; whether to print progress messages (default FALSE)
error_handling	Logical. Should more aggressive error handing be attemptted? Default is false
file_column_names	Names of the columns in the input file (default c("ID1", "ID2", "addRel", "mitRel", "cnuRel"))

Value

NULL. Writes CSV files to disk and updates progress logs.

BGmisc documentation built on Aug. 8, 2025, 7:20 p.m.