dosage_ratios: Calculate the Percentage of Each Dosage Value

In BIGr: Breeding Insight Genomics Functions for Polyploid and Diploid Species

Calculate the Percentage of Each Dosage Value

Description

This function calculates the percentage of each dosage value within a genotype matrix. It assumes that the samples are the columns, and the genomic markers are in rows. Missing data should be set as NA, which will then be ignored for the calculations. All samples must have the same ploidy.

Usage

dosage_ratios(data, ploidy)

Arguments

data	Genotype matrix or data.frame
ploidy	The ploidy of the species being analyzed

Value

A data.frame with percentages of dosage values in the genotype matrix

Examples

# example numeric genotype matrix for a tetraploid
n_ind <- 5
n_snps <- 10

geno <- matrix(as.numeric(sample(0:4, n_ind * n_snps, replace = TRUE)), nrow = n_snps, ncol = n_ind)
colnames(geno) <- paste0("Ind", 1:n_ind)
rownames(geno) <- paste0("SNP", 1:n_snps)
ploidy <- 4

# ratio of dosage value (numeric genotypes) across samples in dataset
result <- dosage_ratios(geno, ploidy)

print(result)

BIGr documentation built on Nov. 5, 2025, 6:03 p.m.