edu.umn.msi.tropix.proteomics.itraqquantitation.impl.WeightedRatiosCalculatorImpl.java Source code

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Here is the source code for edu.umn.msi.tropix.proteomics.itraqquantitation.impl.WeightedRatiosCalculatorImpl.java

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/********************************************************************************
 * Copyright (c) 2009 Regents of the University of Minnesota
 *
 * This Software was written at the Minnesota Supercomputing Institute
 * http://msi.umn.edu
 *
 * All rights reserved. The following statement of license applies
 * only to this file, and and not to the other files distributed with it
 * or derived therefrom.  This file is made available under the terms of
 * the Eclipse Public License v1.0 which accompanies this distribution,
 * and is available at http://www.eclipse.org/legal/epl-v10.html
 *
 * Contributors:
 * Minnesota Supercomputing Institute - initial API and implementation
 *******************************************************************************/

package edu.umn.msi.tropix.proteomics.itraqquantitation.impl;

import com.google.common.base.Function;
import com.google.common.collect.Iterables;
import com.google.common.primitives.Doubles;

class WeightedRatiosCalculatorImpl implements WeightedRatiosCalculator {

    public Ratios computeRatios(final ITraqLabel numLabel, final ITraqLabel denLabel,
            final ReportSummary reportSummary, final Function<Double, Double> weightFunction,
            final boolean normalized) {
        final double[] ratios = new double[reportSummary.getNumGroups()],
                pValues = new double[reportSummary.getNumGroups()];
        int groupNum = 0;
        for (final String groupLabel : reportSummary.getGroups()) {
            final GroupSummary proteinSummary = reportSummary.getGroupSummary(groupLabel);
            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]);
            }

            // final String logRatioStr = Iterables.toString(Doubles.asList(iRatio));
            // System.out.println(logRatioStr);

            if (normalized) {
                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);
            }

            if (pValue < 0) {
                // This hasn't been a problem since upgrading commons-math
                final String ratioStr = Iterables.toString(Doubles.asList(iRatio));
                final String weightsStr = Iterables.toString(Doubles.asList(weights));
                System.out.println(String.format("Negative p-value found for ratios %s and weights %s.", ratioStr,
                        weightsStr));
            }

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

            groupNum++;
        }

        return new Ratios(ratios, pValues);
    }

    public Ratios computeRatios(ITraqLabel numLabel, ITraqLabel denLabel, ReportSummary summary,
            Function<Double, Double> weightFunction) {
        return computeRatios(numLabel, denLabel, summary, weightFunction, false);
    }
}