#' Measure the minor allele frequency of a SNP
#'
#'
measure.maf <- function(x, type = "numeric") {
if (type == "numeric") {
snp.recode <- as.numeric(x) + 1
# Remove NA
snp.recode <- na.omit(snp.recode)
freq <- sum(snp.recode) / (2 * length(snp.recode))
return(min(freq, 1 - freq))
}
if (type == "nucleotide") {
snp.recode <- x[x != "NN"]
snp.recode <- unlist(strsplit(snp.recode, split = ""))
allele.table <- table(snp.recode)
freq <- allele.table / sum(allele.table)
return(min(freq, 1 - freq))
}
}
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