Example usage for org.apache.commons.math.stat.regression SimpleRegression getR

Introduction

In this page you can find the example usage for org.apache.commons.math.stat.regression SimpleRegression getR.

Prototype

public double getR() 

Source Link

Document

Returns <a href="http://mathworld.wolfram.com/CorrelationCoefficient.html"> Pearson's product moment correlation coefficient</a>, usually denoted r.

Usage

From source file:net.sf.mzmine.modules.peaklistmethods.identification.metamsecorrelate.MetaMSEcorrelateTask.java

/**
 * correlates the height profile of one row to another
 * NO escape routine/*from  w  w w. ja  va  2s  .  c o  m*/
 * @param raw
 * @param row
 * @param g
 * @return Pearson r of height correlation
 */
public static double corrRowToRowIProfile(final RawDataFile raw[], PeakListRow row, PeakListRow g) {
    SimpleRegression reg = new SimpleRegression();
    // go through all raw files 
    for (int r = 0; r < raw.length; r++) {
        Feature f1 = row.getPeak(raw[r]);
        Feature f2 = g.getPeak(raw[r]);
        // I profile correlation
        // TODO: low value imputation?
        double I1 = f1 != null ? f1.getHeight() : 0;
        double I2 = f2 != null ? f2.getHeight() : 0;
        reg.addData(I1, I2);
    }
    // TODO weighting of intensity corr
    double corrIprofile = reg.getR();
    return corrIprofile;
}

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From source file:net.sf.mzmine.modules.peaklistmethods.identification.metamsecorrelate.MetaMSEcorrelateTask.java

/**
 * correlates one row to another/*from w  w  w. j  a va  2  s.c o  m*/
 * peak shape correlation (Pearson) (if negative or zero direct escape)
 *       otherwise avg(corr)>= minCorrPeakShape
 * intensity profile correlation (Pearson) >= minCorrIProfile
 *       TODO: maybe impute low values instead of 0 for not detected!
 * @param row
 * @param g
 * @return average correlation over both factors ranging from minR to 1 (or 0 if minimum correlation was not met)
 * @throws Exception 
 */
private double corrRowToRow(final PeakList peakList, final RawDataFile raw[], PeakListRow row, PeakListRow row2)
        throws Exception {
    double corr = 0;
    SimpleRegression reg = new SimpleRegression();
    // count
    int c = 0;
    // go through all raw files 
    for (int r = 0; r < raw.length; r++) {
        Feature f1 = row.getPeak(raw[r]);
        Feature f2 = row2.getPeak(raw[r]);
        if (f1 != null && f2 != null) {
            // peak shape correlation
            FeatureShapeCorrelationData cFS = corrFeatureShape(f1, f2, true);
            if (cFS != null) {
                double tmpcorr = cFS.getR();
                // escape if peak shapes are showing a negative correlation
                if (tmpcorr <= 0)
                    return tmpcorr;
                corr += tmpcorr;
                c++;
            } else {
                // correlation was not possible
                // maybe due to a small peak in this raw file
                // escape if features would be high enough for a correlation
                // this means the features are not intercepting
                if (countDPHigherThanNoise(f1) >= minCorrelatedDataPoints
                        && countDPHigherThanNoise(f2) >= minCorrelatedDataPoints)
                    return 0;
            }
        }
        // I profile correlation
        // TODO: low value imputation?
        double I1 = f1 != null ? f1.getHeight() : 0;
        double I2 = f2 != null ? f2.getHeight() : 0;
        reg.addData(I1, I2);
    }
    // First search for isotopes TODO later fill in isotopes from raw
    int absCharge = AlignedIsotopeGrouperTask.find13CIsotope(peakList, row, row2, maxCharge, mzTolerance);
    boolean isIsotope = absCharge != -1;
    // TODO search for adducts and add correlation: IProfile doesnt have to be the same for adducts
    boolean isAdduct = false;
    if (!isIsotope)
        findAdducts(peakList, row, row2, row.getRowCharge(), row2.getRowCharge());
    double adductBonus = (isIsotope || isAdduct) && useAdductBonusR ? adductBonusR : 0;
    // TODO weighting of intensity corr and feature shape corr
    // there was no correlation possible due to small peaks
    if (c == 0) {
        // 
        return isAdduct || isIsotope ? 1 : 0;
    } else {
        corr = (corr / c);
        double corrIprofile = reg.getR();
        if (corr + adductBonus < minShapeCorrR)
            return 0;
        else if (corrIprofile < minIntensityProfileR)
            return 0;
        else
            return (corr + corrIprofile) / 2;
    }
}

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