Example usage for org.apache.commons.math3.distribution HypergeometricDistribution cumulativeProbability

Introduction

In this page you can find the example usage for org.apache.commons.math3.distribution HypergeometricDistribution cumulativeProbability.

Prototype

public double cumulativeProbability(int x) 

Source Link

Usage

From source file:ch.unil.genescore.pathway.GeneSetLibrary.java

License:asdf

/** Compute enrichment for the given set using hypergeometric distribution (magenta-option)
 *    quantile refers to the cutoff used to assign ins and outs.
 * *//*  w ww  . j  a  v a  2s  .  c o m*/
protected double[] computeHypGeomPvalue2(double[] set, double[] totSet) {
    ArrayList<Double> quantiles = Pascal.set.hypGeomQuantiles_;
    double[] pvals = new double[quantiles.size()];
    if (set.length == 0) {
        for (int i = 0; i < quantiles.size(); i++) {
            pvals[i] = 1;
        }
        return pvals;
    }

    for (int j = 0; j < quantiles.size(); j++) {
        double[] valAr = totSet.clone();
        Arrays.sort(valAr);
        int n = (int) Math.floor(valAr.length * quantiles.get(j));
        double cutoffVal = valAr[n];
        int setSize = valAr.length - n - 1;

        int q = 0;
        for (double g : set) {
            if (g > cutoffVal)
                q += 1;
        }
        HypergeometricDistribution myHypgeom = new HypergeometricDistribution(valAr.length, setSize,
                set.length);
        double pval = 1 - myHypgeom.cumulativeProbability((q - 1));
        pvals[j] = pval;
    }
    return (pvals);
}

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From source file:ch.unil.genescore.pathway.GeneSetLibrary.java

License:asdf

protected void computeHypGeomPvalue(GeneSet set) {
    ArrayList<Double> quantiles = Pascal.set.hypGeomQuantiles_;
    double[] pvals = new double[quantiles.size()];
    if (set.getGenes().size() == 0) {
        for (int i = 0; i < quantiles.size(); i++) {
            pvals[i] = 1;/*  w  ww  . ja v  a2 s .co m*/
        }
        set.setHypGeomPvalues(pvals);
        return;
    }

    for (int j = 0; j < quantiles.size(); j++) {
        double[] valAr = new double[genesForSimulation_.size()];
        for (int i = 0; i < genesForSimulation_.size(); i++) {
            valAr[i] = genesForSimulation_.get(i).getChi2Stat();
        }
        Arrays.sort(valAr);
        int n = (int) Math.floor(valAr.length * quantiles.get(j));
        double cutoffVal = valAr[n];
        int setSize = valAr.length - n - 1;
        HashSet<Gene> pathwayGenes = set.getGenes();
        if (pathwayGenes.size() == 0)
            return;

        int q = 0;
        for (Gene g : pathwayGenes) {
            if (g.getChi2Stat() > cutoffVal)
                q += 1;
        }

        HypergeometricDistribution myHypgeom = new HypergeometricDistribution(valAr.length, setSize,
                pathwayGenes.size());
        double pval = 1 - myHypgeom.cumulativeProbability((q - 1));
        pvals[j] = pval;
    }
    set.setHypGeomPvalues(pvals);
}

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