R/calculate_MAF.R

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

#' Calculate Minor Allele Frequency from a Genotype Matrix
#'
#' 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.
#'
#' @param df Genotype matrix or data.frame
#' @param ploidy The ploidy of the species being analyzed
#' @return 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)
#'
#' @export
calculate_MAF <- function(df, ploidy) {
  if (is.matrix(df)) {
    df <- as.data.frame(df)
  }

  allele_frequencies <- apply(df, 1, function(row) {
    non_na_count <- sum(!is.na(row))
    allele_sum <- sum(row, na.rm = TRUE)
    if (non_na_count > 0) {
      allele_sum / (ploidy * non_na_count)
    } else {
      NA
    }
  })

  maf <- ifelse(allele_frequencies <= 0.5, allele_frequencies, 1 - allele_frequencies)

  df$AF <- allele_frequencies
  df$MAF <- maf

  maf_df <- df[,c("AF", "MAF"), drop = FALSE]

  return(maf_df)
}