calculate_Het: Calculate Observed Heterozygosity from a Genotype Matrix

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

Calculate Observed Heterozygosity from a Genotype Matrix

Description

This function calculates the observed heterozygosity from 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

calculate_Het(geno, ploidy)

Arguments

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

Value

A dataframe of observed heterozygosity values for each sample

Examples

# example input for a diploid
geno <- data.frame(
            Sample1 = c(0, 1, 2, NA, 0),
            Sample2 = c(1, 1, 2, 0, NA),
            Sample3 = c(0, 1, 1, 0, 2),
            Sample4 = c(0, 0, 1, 1, NA)
           )
row.names(geno) <- c("Marker1", "Marker2", "Marker3", "Marker4", "Marker5")

ploidy <- 2

# calculate observed heterozygosity
result <- calculate_Het(geno, ploidy)

print(result)

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