#' @title Mean and SD of SNP Genotypes
#'
#' @param ... Additional arguments passed to PLINK.
#'
#' @export
mean.sd <- function(...) {
#### Get mean and SD of the SNP genotypes in (0/1/2) coding ####
freqx <- plink(cmd="--freqx", ...)
freqx2 <- read.table.plink(freqx, ".frqx", sep="\t")
data <- as.matrix(freqx2[, c("C.HOM.A1.", "C.HET.", "C.HOM.A2.")])
n <- rowSums(data)
sumx <- data %*% c(2,1,0)
meanx <- as.vector(sumx / n)
sumx2 <- data %*% c(4,1,0)
var <- as.vector(sumx2)/n - meanx^2
var <- var * (n-1)/n
maf <- 0.5 - abs(meanx - 1) / 2
return(cbind(freqx2, data.frame(mean=meanx, maf=maf,
var=var, sd=sqrt(var))))
}
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