BIGr (version 0.6.2)

allele_freq_poly: Compute Allele Frequencies for Populations

Description

Computes allele frequencies for specified populations given SNP array data

Usage

allele_freq_poly(geno, populations, ploidy = 2)

Value

data.frame consisting of allele_frequencies for populations (columns) for each SNP (rows)

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

ploidy

integer indicating the ploidy level (default is 2 for diploid)

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

# Example inputs
geno_matrix <- matrix(
c(4, 1, 4, 0, # S1
  2, 2, 1, 3, # S2
  0, 4, 0, 4, # S3
  3, 3, 2, 2, # S4
  1, 4, 2, 3),# S5
nrow = 4, ncol = 5, byrow = FALSE, # individuals=rows, SNPs=cols
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)