R/qstats.r

In kokrah/qsmooth: Smooth quantile normalization

#' Compute quantile statistics
#' 
#' @param exprs for counts use log2(raw counts + 1)), for MA use log2(raw intensities)
#' @param groups groups to which samples belong (character vector)
#' @param window window size for running median as a fraction on the number of rows of exprs
qstats = function (exprs, groups, window) {
  
  # Compute sample quantiles
  Q = apply(exprs, 2, sort) 
  
  # Compute quantile reference
  Qref = rowMeans(Q)  
  
  # Compute SST
  SST = rowSums((Q - Qref)^2)
  
  # Compute SSB
  f = factor(as.character(groups))
  X = model.matrix(~ 0 + f)
  QBETAS = t(solve(t(X) %*% X) %*% t(X) %*% t(Q))
  Qhat = QBETAS %*% t(X)
  SSB = rowSums((Qhat - Qref)^2)
  
  # Compute weights
  roughWeights = 1 - SSB / SST
  roughWeights[SST < 1e-6] = 1
  
  # Compute smooth weights
  k = floor(window * nrow(Q))
  if (k %% 2 == 0) k = k + 1
  smoothWeights = runmed(roughWeights, k = k, endrule="constant")
  
  list(Q=Q, Qref=Qref, Qhat=Qhat, QBETAS=QBETAS, SST=SST, SSB=SSB, SSE=SST-SSB,
       roughWeights=roughWeights, smoothWeights=smoothWeights)
}