stabilizecounts.cpp

#include <Rcpp.h>

//compute variance with bessel correction for a single bin
inline double binValue(int* counts, int len){
  long tot = 0;
  long tot2 = 0;
  double denom = len;
  for (int i = 0; i < len; ++i){
    int c = counts[i];
    tot += c;
    tot2 += c*c;
  }
  double mean = tot/denom;
  double var = (tot2 - mean*mean*denom)/(denom-1);
  return mean/sqrt(var);
}

// [[Rcpp::export]]
Rcpp::NumericVector stabilizeBins(Rcpp::IntegerVector sig, int binsize){

  int* C = sig.begin();
  int siglen = sig.length();
  int nbins = siglen / binsize;
  bool incompleteBin = siglen % binsize != 0;
  Rcpp::NumericVector binnedSig(nbins + (incompleteBin?1:0));
  //loop on the bins
  int bin = 0;
  for (; bin < nbins; ++bin){
    binnedSig[bin] = binValue(C + bin*binsize, binsize);
  }
  if (incompleteBin) {
    binnedSig[nbins] = binValue(C + nbins*binsize, siglen - nbins*binsize);
  }

  return binnedSig;
}