The calc_dm function implements the distance-to-the-median measurement from Kolodziejczyk et. al. (Cell Stem Cell, 2015).

distance-to-median.R

library(zoo)
calc_dm = function(expr, func=median) {
  if( is.null(rownames(expr)) ) { rownames(expr) = 1:nrow(expr) }
  
  # Calculate log10 mean of the rows
  m = log10(rowMeans(expr))
  names(m) = rownames(expr)
  
  # Calculate the squared cv
  cv2 = apply(expr, 1, function(x) { (sd(x)/mean(x))^2 })
  
  # Sort the means
  s = names(sort(m))
  
  # Calculate median squared cv in a window of 50 genes
  r = rollapply(data = log10(cv2[s]), width = 50, FUN=func, fill="extend")
  names(r) = s
  
  # Return distance to the median
  log10(cv2) - r[names(cv2)]
}

Application on data from mouse single ES cells from Mantsoki et. al. (Comp. Biol. Chem, 2016)