Example usage for org.apache.commons.math3.stat.descriptive.moment Variance clear

Introduction

In this page you can find the example usage for org.apache.commons.math3.stat.descriptive.moment Variance clear.

Prototype

@Override
public void clear() 

Source Link

Usage

From source file:nl.systemsgenetics.genenetworkbackend.hpo.TestDiseaseGenePerformance.java

private static HashMap<String, MeanSd> calculatePathayMeansOfAnnotatedGenes(
        DoubleMatrixDataset<String, String> predictionMatrixSignificant,
        DoubleMatrixDataset<String, String> annotationMatrixSignificant) {

    HashMap<String, MeanSd> pathwayMeanSdMap = new HashMap<>(predictionMatrixSignificant.columns());

    Mean meanCalculator = new Mean();
    Variance varianceCalculator = new Variance();

    for (String pathway : predictionMatrixSignificant.getColObjects()) {

        meanCalculator.clear();/*from www .  ja v a2 s.  c o  m*/
        varianceCalculator.clear();

        DoubleMatrix1D pathwayPredictions = predictionMatrixSignificant.getCol(pathway);
        DoubleMatrix1D pathwayAnnotations = annotationMatrixSignificant.getCol(pathway);

        for (int g = 0; g < pathwayPredictions.size(); ++g) {
            if (pathwayAnnotations.get(g) != 0) {
                meanCalculator.increment(pathwayPredictions.getQuick(g));
                varianceCalculator.increment(pathwayPredictions.getQuick(g));
            }
        }

        double v = varianceCalculator.getResult();

        pathwayMeanSdMap.put(pathway, new MeanSd(meanCalculator.getResult(), v * v));

    }

    return pathwayMeanSdMap;

}

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