validate_pedigree: Validate Pedigree Trios Using Mendelian Error Analysis

In BIGpopA: Pedigree Validation Genetic Composition of Diploids & Polyploids

Validate Pedigree Trios Using Mendelian Error Analysis

Description

Validates parent-offspring trios against SNP genotype data using Mendelian error rates. Identifies incorrect parentage assignments, suggests best-matching replacements, and outputs a corrected pedigree. Founder trios (both parents coded as 0) are preserved unchanged if a founders file is supplied. Trios absent from the genotype file are retained as no_genotype_data.

Usage

validate_pedigree(
  pedigree_file,
  genotypes_file,
  founders_file = NULL,
  trio_error_threshold = 5,
  min_markers = 10,
  single_parent_error_threshold = 2,
  verbose = TRUE,
  plot_results = TRUE
)

Arguments

pedigree_file	Path to the pedigree file (TSV/CSV/TXT), OR a data.frame / data.table with columns: id, male_parent, female_parent.
genotypes_file	Path to the genotypes file (TSV/CSV/TXT), OR a data.frame / data.table with an id column followed by marker columns coded as 0, 1, 2.
founders_file	Character, optional. Path to a one-column file listing founder IDs. Founders with both parents coded as 0 are left unchanged. Defaults to NULL.
trio_error_threshold	Numeric. Maximum Mendelian error percentage to classify a trio as pass (default: 5.0). Must be between 0 and 100.
min_markers	Integer. Minimum non-missing markers required to evaluate a trio (default: 10).
single_parent_error_threshold	Numeric. Maximum homozygous-marker mismatch percentage for a parent to be considered acceptable (default: 2.0). Must be between 0 and 100.
verbose	Logical. If TRUE, prints progress, summary, and results to the console (default: TRUE).
plot_results	Logical. If TRUE, prints a histogram of trio Mendelian error percentages with a threshold line (default: TRUE).

Value

An invisible named list with the following elements:

pass

Trios that passed the Mendelian error threshold.

fail

Trios that failed the Mendelian error threshold.

low_markers

Trios with insufficient markers for evaluation.

no_genotype_data

Trios absent from the genotype file.

founders

Trios identified as founders.

missing_parents

Trios with one or both parents coded as 0 (non-founders).

full_results

Complete data.table with all trios and all output columns.

corrected_pedigree

Pedigree table after applying recommended corrections.

plot

ggplot object if plot_results = TRUE, otherwise NULL.

Author(s)

Josue Chinchilla-Vargas

Examples

geno_df <- data.frame(
  id  = c("P1", "P2", "P3", "Off1", "Off2"),
  S1  = c(0L, 2L, 0L, 1L, 0L),
  S2  = c(2L, 0L, 2L, 1L, 2L),
  S3  = c(0L, 2L, 0L, 1L, 0L),
  S4  = c(2L, 0L, 2L, 1L, 2L),
  S5  = c(0L, 2L, 0L, 1L, 0L),
  S6  = c(2L, 0L, 2L, 1L, 2L),
  S7  = c(0L, 2L, 0L, 1L, 0L),
  S8  = c(2L, 0L, 2L, 1L, 2L),
  S9  = c(0L, 2L, 0L, 1L, 0L),
  S10 = c(2L, 0L, 2L, 1L, 2L)
)

ped_df <- data.frame(
  id            = c("Off1", "Off2"),
  male_parent   = c("P1",   "P1"),
  female_parent = c("P2",   "P3"),
  stringsAsFactors = FALSE
)

results <- validate_pedigree(
  pedigree_file  = ped_df,
  genotypes_file = geno_df,
  verbose        = FALSE,
  plot_results   = FALSE
)
print(results$full_results)

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