gistfile1.java

  public Ratios computeRatios(final ITraqLabel numLabel, final ITraqLabel denLabel, final ReportSummary reportSummary,
      final Function<Double, Double> weightFunction) {
    final double[] ratios = new double[reportSummary.getNumProteins()], pValues = new double[reportSummary.getNumProteins()];
    int proteinNum = 0;
    for(final String protein : reportSummary.getProteins()) {
      final ProteinSummary proteinSummary = reportSummary.getProteinSummary(protein);
      final double[] iRatio = new double[proteinSummary.getNumEntries()];
      final double[] num = proteinSummary.getIntensities(numLabel);
      final double[] den = proteinSummary.getIntensities(denLabel);

      double[] weights = proteinSummary.getLogIntensitiesProducts();
      if(weightFunction != null) {
        final double[] modifiedWeights = new double[weights.length];
        for(int i = 0; i < weights.length; i++) {
          modifiedWeights[i] = weightFunction.apply(weights[i]);
        }
        weights = modifiedWeights;
      }

      for(int i = 0; i < iRatio.length; i++) {
        iRatio[i] = Math.log(num[i] / den[i]);
      }
      
      if(normalizeRatios) {
        final double median = RUtils.median(iRatio);
        for(int i = 0; i < iRatio.length; i++) {
          iRatio[i] = iRatio[i] / median;
        }        
      }

      final double iRatioW1 = RUtils.weightedMean(iRatio, weights);
      final double iRatioW = Math.exp(iRatioW1);
      double pValue = 2.0;
      if(iRatio.length > 2) {
        pValue = RMethods.getWeightedPValue(iRatio, weights);
      }

      ratios[proteinNum] = iRatioW;
      pValues[proteinNum] = pValue;

      proteinNum++;
    }

    return new Ratios(ratios, pValues);
  }