Allele frequency calc from a genotype matrix

#The genotype matrix has individuals in rows and mutations #in columns, with a 0,1, or 2 entered for the number of #alternate alleles in the diploid

# Let’s create a matrix with 5 individuals, 10 SNPS, and some missing data:
set.seed(345)
GEN = matrix(sample(0:2, 50, replace=TRUE), nrow=5, ncol=10)
GEN[5,1] <- NA
GEN

# Function to calculate the allele frequency of a column
af <- function(i, gen){
	sum(gen[,i], na.rm=TRUE)/(2*sum(!is.na(gen[,i])))
}
af(1, GEN)

# Code to calculate the allele frequencies of all SNPs in the GEN matrix
apply(GEN, 2, function(i){
    sum(i, na.rm=TRUE)/(2*sum(!is.na(i)))})