solve_composition_poly: Compute Genome-Wide Breed Composition

In BIGpopA: Pedigree Validation Genetic Composition of Diploids & Polyploids

Compute Genome-Wide Breed Composition

Description

Computes genome-wide breed/ancestry composition using quadratic programming on a batch of animals.

Usage

solve_composition_poly(
  Y,
  X,
  ped = NULL,
  groups = NULL,
  mia = FALSE,
  sire = FALSE,
  dam = FALSE,
  ploidy = 2
)

Arguments

Y	numeric matrix of genotypes (columns) from all animals (rows) in the population, coded as dosage of allele B (0, 1, 2, ..., ploidy).
X	numeric matrix of allele frequencies (rows) from each reference panel (columns). Frequencies are relative to allele B.
ped	data.frame giving pedigree information. Must be formatted with columns: ID, Sire, Dam.
groups	list of IDs categorized by breed/population. If specified, output will be a list of results categorized by breed/population.
mia	logical. Only applies if ped argument is supplied. If TRUE, returns a data.frame containing the inferred maternally inherited allele for each locus for each animal instead of breed composition results.
sire	logical. Only applies if ped argument is supplied. If TRUE, returns a data.frame containing sire genotypes for each locus for each animal instead of breed composition results.
dam	logical. Only applies if ped argument is supplied. If TRUE, returns a data.frame containing dam genotypes for each locus for each animal instead of breed composition results.
ploidy	integer. The ploidy level of the species (e.g., 2 for diploid, 3 for triploid).

Value

A data.frame, or a list of data.frames when groups is not NULL, containing breed/ancestry composition results.

References

Funkhouser SA, Bates RO, Ernst CW, Newcom D, Steibel JP. Estimation of genome-wide and locus-specific breed composition in pigs. Transl Anim Sci. 2017 Feb 1;1(1):36-44.

Examples

allele_freqs_matrix <- matrix(
  c(0.625, 0.500,
    0.500, 0.500,
    0.500, 0.500,
    0.750, 0.500,
    0.625, 0.625),
  nrow = 5, ncol = 2, byrow = TRUE,
  dimnames = list(paste0("SNP", 1:5), c("VarA", "VarB"))
)

val_geno_matrix <- matrix(
  c(2, 1, 2, 3, 4,
    3, 4, 2, 3, 0),
  nrow = 2, ncol = 5, byrow = TRUE,
  dimnames = list(paste0("Test", 1:2), paste0("SNP", 1:5))
)

composition <- solve_composition_poly(Y = val_geno_matrix,
                                      X = allele_freqs_matrix,
                                      ploidy = 4)
print(composition)

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