calculate_MAF: Calculate Minor Allele Frequency from a Genotype Matrix

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

Calculate Minor Allele Frequency from a Genotype Matrix

Description

This function calculates the allele frequency and minor allele frequency 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_MAF(df, ploidy)

Arguments

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

Value

A dataframe of AF and MAF values for each marker

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 allele frequency
result <- calculate_MAF(geno, ploidy)

print(result)

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