check_ped: Check and Correct Common Pedigree Errors

In BIGpopA: Pedigree Validation Genetic Composition of Diploids & Polyploids

Check and Correct Common Pedigree Errors

Description

Reads a 3-column pedigree file (id, male_parent, female_parent) and performs quality checks, optionally correcting detected errors. Exact duplicates and missing parents are always corrected. Conflicting trios and inconsistent sex roles are corrected when their respective arguments are TRUE. Cycles are reported only and must be resolved manually.

Usage

check_ped(
  ped.file,
  seed = NULL,
  verbose = TRUE,
  correct_conflicting_trios = TRUE,
  correct_inconsistent_sex_roles = TRUE
)

Arguments

ped.file	Path to the pedigree text file (TSV/CSV/TXT), OR a data.frame / data.table with columns: id, male_parent, female_parent.
seed	Optional integer seed for reproducibility. Pass NULL (default) to skip setting a seed.
verbose	Logical. If TRUE (default), prints the report to the console.
correct_conflicting_trios	Logical. If TRUE (default), sets conflicting male_parent and female_parent to 0 and collapses to one row per ID.
correct_inconsistent_sex_roles	Logical. If TRUE (default), sets male_parent and female_parent to 0 for rows involving IDs found as both, then removes any resulting exact duplicates.

Value

An invisible named list of data frames:

exact_duplicates

Exact duplicate rows found in the input.

conflicting_trios

IDs with conflicting male_parent or female_parent assignments.

inconsistent_sex_roles

Rows where a conflicting ID appears as male_parent or female_parent.

missing_parents

Parent IDs absent from id, added as founders.

dependencies

Cycles detected in the pedigree. Must be resolved manually.

corrected_pedigree

Corrected pedigree table.

Author(s)

Josue Chinchilla-Vargas

Examples

# Self-contained example using a data.frame
ped_df <- data.frame(
  id            = c("A", "B", "C", "C", "D"),
  male_parent   = c("0", "0", "A", "A", "B"),
  female_parent = c("0", "0", "B", "B", "C"),
  stringsAsFactors = FALSE
)
ped_errors <- check_ped(ped.file = ped_df, seed = 101919, verbose = FALSE)
names(ped_errors)
head(ped_errors$corrected_pedigree)


library(data.table)
ped_dt <- data.table(id = c("A", "B", "C"),
                     male_parent   = c("0", "0", "A"),
                     female_parent = c("0", "0", "B"))
ped_errors <- check_ped(ped.file = ped_dt, verbose = FALSE)

BIGpopA documentation built on July 17, 2026, 1:07 a.m.