allele_freq_poly: Compute Allele Frequencies for Populations

In BIGpopA: Pedigree Validation Genetic Composition of Diploids & Polyploids

Compute Allele Frequencies for Populations

Description

Computes allele frequencies for specified populations given SNP array data.

Usage

allele_freq_poly(geno, populations, ploidy = 2)

Arguments

geno	matrix of genotypes coded as the dosage of allele B (0, 1, 2, ..., ploidy) with individuals in rows (named) and SNPs in columns (named).
populations	list of named populations. Each population has a vector of IDs that belong to the population. Allele frequencies will be derived from all animals in each population.
ploidy	integer indicating the ploidy level (default is 2 for diploid).

Value

A matrix of allele frequencies with SNPs in rows and populations in columns.

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

geno_matrix <- matrix(
  c(4, 1, 4, 0,
    2, 2, 1, 3,
    0, 4, 0, 4,
    3, 3, 2, 2,
    1, 4, 2, 3),
  nrow = 4, ncol = 5, byrow = FALSE,
  dimnames = list(paste0("Ind", 1:4), paste0("S", 1:5))
)

pop_list <- list(
  PopA = c("Ind1", "Ind2"),
  PopB = c("Ind3", "Ind4")
)

allele_freqs <- allele_freq_poly(geno = geno_matrix,
                                 populations = pop_list,
                                 ploidy = 4)
print(allele_freqs)

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