R/maf.R

In HardyWeinberg: Statistical Tests and Graphics for Hardy-Weinberg Equilibrium

`maf` <- function(x) {
  # compute the minor allele frequency for a vector or for each row of a matrix.
  if(is.vector(x)) {
   p <- (x[1]+0.5*x[2])/sum(x)
   y <- min(p,1-p)
  } else
  if(is.matrix(x)) {
   p <- (x[,1]+0.5*x[,2])/apply(x,1,sum)
   y <- pmin(p,1-p)
  }
  return(y)
}