BIGpopA
Pedigree Validation Genetic Composition of Diploids & Polyploids
Tools for pedigree quality control and genomic breed/line
composition estimation in diploid and polyploid breeding populations.
'BIGpopA' provides functions to check and correct common pedigree
errors, assign parentage from SNP genotype data using Mendelian error
rates, validate parent-offspring trios, and estimate genome-wide
breed or line composition using quadratic programming. Pedigree
validation and parentage assignment support any ploidy, using a
polysomic Mendelian test for even ploidy and a homozygosity-based
check for odd ploidy. Genotypes can be supplied as dosage tables, VCF
files, or 'PLINK' .ped files. For more details about the included
'breedTools' functions, see Funkhouser et al. (2017)
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.