R/normalizeNetwork.R

In SCORPION: Single Cell Oriented Reconstruction of PANDA Individual Optimized Networks

normalizeNetwork <- function(X) {

  nr = nrow(X)
  nc = ncol(X)
  dm = c(nr, nc)

  # overall values
  mu0 = mean(X)
  std0 = sd(X) * sqrt((nr * nc - 1) / (nr * nc))

  # operations on rows
  mu1 = rowMeans(X) # operations on rows
  std1 = rowSds(X) * sqrt((nc - 1) / nc)

  mu1 = rep(mu1, nc)
  dim(mu1) = dm
  std1 = rep(std1, nc)
  dim(std1) = dm

  Z1 = (X - mu1) / std1

  # operations on columns
  mu2 = colMeans(X) # operations on columns
  std2 = colSds(X) * sqrt((nr - 1) / nr)

  mu2 = rep(mu2, each = nr)
  dim(mu2) = dm
  std2 = rep(std2, each = nr)
  dim(std2) = dm

  Z2 = (X - mu2) / std2

  # combine and return
  normMat = Z1 / sqrt(2) + Z2 / sqrt(2)

  Z0=(X-mu0)/std0;
  f1=is.na(Z1@x)
  f2=is.na(Z2@x);


  normMat@x[f1]=Z2@x[f1]/sqrt(2)+Z0@x[f1]/sqrt(2);
  normMat@x[f2]=Z1@x[f2]/sqrt(2)+Z0@x[f2]/sqrt(2);
  normMat@x[f1 & f2]=2*Z0@x[f1 & f2]/sqrt(2);

  return(normMat)
}