find_parentage: Find Parentage Assignments for Progeny

In BIGpopA: Pedigree Validation Genetic Composition of Diploids & Polyploids

Find Parentage Assignments for Progeny

Description

Assigns the most likely parent(s) to each progeny from SNP genotype data using Mendelian error rates or homozygous mismatch rates. Parents or progeny absent from the genotype file are removed with a warning.

Usage

find_parentage(
  genotypes_file,
  parents_file,
  progeny_file,
  method = "best_pair",
  min_markers = 10,
  error_threshold = 5,
  show_ties = TRUE,
  allow_parent_selfing = FALSE,
  exclude_self_match = TRUE,
  verbose = TRUE,
  plot_results = TRUE
)

Arguments

genotypes_file	Path to a TSV/CSV/TXT file, OR a data.frame / data.table with an 'id' column followed by marker columns coded as 0, 1, 2.
parents_file	Path to a TSV/CSV/TXT file, OR a data.frame / data.table with an 'id' column and an optional 'sex' column ('M', 'F', or 'A'). If absent, all parents are treated as ambiguous.
progeny_file	Path to a TSV/CSV/TXT file, OR a data.frame / data.table with an 'id' column.
method	Character. One of "best_male_parent", "best_female_parent", "best_match", or "best_pair" (default).
min_markers	Integer. Minimum markers required; fewer flags low_markers (default: 10).
error_threshold	Numeric. Maximum mismatch percentage; exceeded values flag high_error (default: 5.0). Must be between 0 and 100.
show_ties	Logical. If TRUE, tied best pairs are appended as suffix columns. Default is TRUE.
allow_parent_selfing	Logical. If FALSE, candidate pairs with identical male and female parent IDs are excluded. Applies only when method is "best_pair". Default is FALSE.
exclude_self_match	Logical. If TRUE, each progeny ID is excluded from its own candidate parent set, preventing self-matches when progeny are also present in the parents file. Default is TRUE.
verbose	Logical. If TRUE, prints progress and summary. Default is TRUE.
plot_results	Logical. If TRUE, plots the Mendelian error distribution. Requires ggplot2. Default is TRUE.

Value

A named list (returned invisibly) with elements:

pass

Progeny with a confident parentage assignment.

high_error

Progeny whose best assignment exceeds the error threshold.

low_markers

Progeny with insufficient markers for a valid assignment.

full_results

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

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)
)

parents_df <- data.frame(
  id  = c("P1", "P2", "P3"),
  sex = c("M",  "F",  "F"),
  stringsAsFactors = FALSE
)

progeny_df <- data.frame(
  id = c("Off1", "Off2"),
  stringsAsFactors = FALSE
)

results <- find_parentage(
  genotypes_file = geno_df,
  parents_file   = parents_df,
  progeny_file   = progeny_df,
  method         = "best_pair",
  verbose        = FALSE,
  plot_results   = FALSE
)
print(results$full_results)

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