sliceFamilies: sliceFamilies

In R-Computing-Lab/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.

R-Computing-Lab/BGMisc documentation built on July 16, 2025, 9:09 p.m.