BIGr (version 0.6.2)

dosage_ratios: 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)

Value

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

Arguments

data

Genotype matrix or data.frame

ploidy

The ploidy of the species being analyzed

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)