BIGpopa_logo

Breeding Insight Genomics population Analyses

Pedigree Validation and Breed/Line Composition Estimation for Diploid and Polyploid Species

BIGpopA is an R package developed by Breeding Insight that provides tools for pedigree quality control and genomic breed/line composition estimation in diploid and polyploid breeding populations. It is designed to help researchers and breeders identify pedigree errors, assign parentage from SNP genotype data, and estimate genome-wide breed or line composition.

Installation

To install the latest CRAN version of BIGpopA:

install.packages("BIGpopA")
library(BIGpopA)

To install the development version of BIGpopA, install from GitHub using remotes:

install.packages("remotes")
remotes::install_github("Breeding-Insight/BIGpopA", dependencies = TRUE)
library(BIGpopA)

Note: BIGpopA is currently in development. Please report any bugs or issues on the GitHub Issues page.

Main functions

Function	Purpose
`check_ped()`	Detect and correct pedigree errors (duplicates, conflicting trios, missing parents, cycles, inconsistent sex roles)
`validate_pedigree()`	Validate parent-offspring trios against SNP genotypes using Mendelian error rates
`find_parentage()`	Assign the most likely parent(s) to progeny from candidate parents
`allele_freq_poly()`	Compute reference population allele frequencies
`solve_composition_poly()`	Estimate genome-wide breed/line composition by quadratic programming
`vcf_to_dosage()`	Convert a VCF (`.vcf` / `.vcf.gz`) to allele dosages for any ploidy
`ped_to_dosage()`	Convert a PLINK `.ped` (with optional `.map`) to allele dosages

Pedigree validation and parentage assignment support any ploidy, using a polysomic Mendelian test for even ploidy and a homozygosity-based check for odd ploidy.

Genotype input formats

validate_pedigree(), find_parentage(), allele_freq_poly() and solve_composition_poly() accept genotypes in any of these formats:

Format	Notes
Text file (`.txt`, `.tsv`, `.csv`)	ID column followed by marker columns coded as allele-B dosage (0, 1, …, ploidy)
VCF (`.vcf`, `.vcf.gz`) or `vcfR` object	`GT` calls converted to ALT-allele dosage using the function’s `ploidy`
PLINK `.ped` (+ optional `.map`)	Diploid only; the `.map` supplies marker names
`data.frame` / `data.table` / `matrix`	Already-loaded dosage data

# Same call, different input formats
find_parentage("genotypes.vcf.gz", "parents.txt", "progeny.txt", ploidy = 4)
find_parentage("genotypes.ped",    "parents.txt", "progeny.txt")

# Breed/line composition from a reference and a validation VCF
freq <- allele_freq_poly("reference.vcf", populations, ploidy = 2)
comp <- solve_composition_poly("validation.vcf", freq, ploidy = 2)

Shiny app

BIGpopA powers the pedigree and composition modules of Familia, a point-and-click interface for the same analyses.

Funding

BIGpopA development is supported by Breeding Insight, a USDA-funded initiative based at the University of Florida - IFAS.

Citation

If you use BIGpopA in your research, please cite as:

Chinchilla-Vargas, Josue, and Breeding Insight Team. 2026. “BIGpopA: Pedigree Validation and Breed/Line Composition Estimation for Diploid and Polyploid Species.” R package version 2.1.0. https://github.com/Breeding-Insight/BIGpopA.