Examples with DoubleArrayList cern.colt.list.DoubleArrayList used on opensource projects

Example 51 with DoubleArrayList

use of cern.colt.list.DoubleArrayList in project Gemma by PavlidisLab.

the class SpearmanMetricsTest method testCorrelWithMissing.

/**
 * See testCorrelB for the same numbers tested a different way (with no missing values)
 */
@Test
public void testCorrelWithMissing() {
    // note the nominal tie in one (20)
    double[] a = new double[] { 400, 43, 310, 20, 20, 688, 498, 533, 723, 1409, 1500 };
    double[] b = new double[] { 1545, 1287, 2072, 1113, 676, 2648, 2478, 2574, 3554, 5155, 1624 };
    boolean[] usedA = new boolean[] { true, false, true, true, true, true, true, true, false, true, true };
    boolean[] usedB = new boolean[] { true, true, true, true, true, true, true, true, false, true, true };
    assertEquals(a.length, b.length);
    assertEquals(a.length, usedA.length);
    assertEquals(b.length, usedB.length);
    DoubleArrayList ranksIA = Rank.rankTransform(new DoubleArrayList(a));
    DoubleArrayList ranksIB = Rank.rankTransform(new DoubleArrayList(b));
    SpearmanMetrics test = new SpearmanMetrics(10);
    double actualValue = test.spearman(ranksIA.elements(), ranksIB.elements(), usedA, usedB, 0, 1);
    double expectedValue = 0.7113033;
    assertEquals(expectedValue, actualValue, 0.0001);
}

Example 52 with DoubleArrayList

use of cern.colt.list.DoubleArrayList in project Gemma by PavlidisLab.

the class CoexpressionServiceImpl method computeRelativeRanks.

private Map<Long, List<Double>> computeRelativeRanks(TreeMap<Integer, Map<Long, Integer>> forRanks) {
    Map<Long, List<Double>> relRanks = new HashMap<>();
    for (Integer support : forRanks.keySet()) {
        // low ranks = low node degree = good.
        Map<Long, Double> rt = Rank.rankTransform(forRanks.get(support));
        double max = DescriptiveWithMissing.max(new DoubleArrayList(ArrayUtils.toPrimitive(new ArrayList<>(rt.values()).toArray(new Double[] {}))));
        for (Long g : rt.keySet()) {
            double relRank = rt.get(g) / max;
            if (!relRanks.containsKey(g)) {
                relRanks.put(g, new ArrayList<Double>());
            }
            // the ranks are in order.
            relRanks.get(g).add(relRank);
        }
    }
    return relRanks;
}

Example 53 with DoubleArrayList

use of cern.colt.list.DoubleArrayList in project Gemma by PavlidisLab.

the class ExpressionExperimentQCController method removeMVOutliers.

/**
 * Remove outliers from the MeanVarianceRelation by removing those points which have: (zscore(mean) > zscoreMax ||
 * zscore(variance) > zscoreMax)
 */
@SuppressWarnings("unused")
private MeanVarianceRelation removeMVOutliers(MeanVarianceRelation mvr, double zscoreMax) {
    MeanVarianceRelation ret = MeanVarianceRelation.Factory.newInstance();
    ByteArrayConverter bac = new ByteArrayConverter();
    DoubleArrayList vars = new DoubleArrayList(bac.byteArrayToDoubles(mvr.getVariances()));
    DoubleArrayList means = new DoubleArrayList(bac.byteArrayToDoubles(mvr.getMeans()));
    DoubleArrayList filteredMeans = new DoubleArrayList();
    DoubleArrayList filteredVars = new DoubleArrayList();
    DoubleArrayList zVars = this.zscore(vars);
    DoubleArrayList zMeans = this.zscore(means);
    // clip outliers
    for (int i = 0; i < zMeans.size(); i++) {
        if (Math.abs(zMeans.getQuick(i)) > zscoreMax || Math.abs(zVars.getQuick(i)) > zscoreMax) {
            continue;
        }
        filteredMeans.add(means.getQuick(i));
        filteredVars.add(vars.getQuick(i));
    }
    log.debug(filteredMeans.size() + " (out of " + means.size() + ") MV points had mean or variance zscore < " + zscoreMax + ". Max mean,variance is ( " + Descriptive.max(filteredMeans) + "," + Descriptive.max(filteredVars) + ").");
    ret.setVariances(bac.doubleArrayToBytes(filteredVars));
    ret.setMeans(bac.doubleArrayToBytes(filteredMeans));
    return ret;
}

Example 54 with DoubleArrayList

use of cern.colt.list.DoubleArrayList in project Gemma by PavlidisLab.

the class ExpressionExperimentQCController method zscore.

/**
 * @return zscores
 */
private DoubleArrayList zscore(DoubleArrayList d) {
    DoubleArrayList z = new DoubleArrayList();
    double mean = Descriptive.mean(d);
    double sd = Descriptive.standardDeviation(Descriptive.variance(d.size(), Descriptive.sum(d), Descriptive.sumOfSquares(d)));
    for (int i = 0; i < d.size(); i++) {
        z.add(Math.abs(d.getQuick(i) - mean) / sd);
    }
    assert z.size() == d.size();
    return z;
}

Example 55 with DoubleArrayList

use of cern.colt.list.DoubleArrayList in project tdq-studio-se by Talend.

the class AbstractDoubleIntMap method keys.

/**
 * Returns a list filled with all keys contained in the receiver.
 * The returned list has a size that equals <tt>this.size()</tt>.
 * Note: Keys are filled into the list in no particular order.
 * However, the order is <i>identical</i> to the order used by method {@link #forEachKey(DoubleProcedure)}.
 * <p>
 * This method can be used to iterate over the keys of the receiver.
 *
 * @return the keys.
 */
public DoubleArrayList keys() {
    DoubleArrayList list = new DoubleArrayList(size());
    keys(list);
    return list;
}