Examples with RealMatrix org.apache.commons.math3.linear.RealMatrix used on opensource projects

Example 41 with RealMatrix

use of org.apache.commons.math3.linear.RealMatrix in project gatk by broadinstitute.

the class DecomposeSingularValuesIntegrationTest method assertOutputFile.

private void assertOutputFile(final File outputFile, final int gtNumRows, final int gtNumCols) {
    Assert.assertTrue(outputFile.exists(), "Output file does not exist.");
    Assert.assertTrue(outputFile.length() > 0, "Output file is empty: " + outputFile.getAbsolutePath());
    final RealMatrix actualResults = PoNTestUtils.readTsvIntoMatrix(outputFile);
    Assert.assertEquals(actualResults.getRowDimension(), gtNumRows);
    Assert.assertEquals(actualResults.getColumnDimension(), gtNumCols);
}

Example 42 with RealMatrix

use of org.apache.commons.math3.linear.RealMatrix in project gatk by broadinstitute.

the class NormalizeSomaticReadCountsIntegrationTest method assertTangentNormalized.

private void assertTangentNormalized(final ReadCountCollection actualReadCounts, final ReadCountCollection preTangentNormalized, final RealMatrix betaHats, final File ponFile) {
    try (final HDF5File ponReader = new HDF5File(ponFile)) {
        final PCACoveragePoN pon = new HDF5PCACoveragePoN(ponReader);
        final RealMatrix inCounts = reorderTargetsToPoNOrder(preTangentNormalized, pon.getPanelTargetNames());
        final RealMatrix actual = reorderTargetsToPoNOrder(actualReadCounts, pon.getPanelTargetNames());
        final RealMatrix ponMat = pon.getReducedPanelCounts();
        final RealMatrix projection = ponMat.multiply(betaHats);
        final RealMatrix expected = inCounts.subtract(projection);
        Assert.assertEquals(actual.getRowDimension(), expected.getRowDimension());
        Assert.assertEquals(actual.getColumnDimension(), expected.getColumnDimension());
        for (int i = 0; i < actual.getRowDimension(); i++) {
            Assert.assertEquals(actual.getRow(i), expected.getRow(i));
        }
    }
}

Example 43 with RealMatrix

use of org.apache.commons.math3.linear.RealMatrix in project gatk by broadinstitute.

the class NormalizeSomaticReadCountsIntegrationTest method assertBetaHats.

/**
     * Asserts that a collection of beta-hats corresponds to the expected value given
     * the input pre-tangent normalization matrix and the PoN file.
     */
private void assertBetaHats(final ReadCountCollection preTangentNormalized, final RealMatrix actual, final File ponFile) {
    Assert.assertEquals(actual.getColumnDimension(), preTangentNormalized.columnNames().size());
    final double epsilon = PCATangentNormalizationUtils.EPSILON;
    try (final HDF5File ponReader = new HDF5File(ponFile)) {
        final PCACoveragePoN pon = new HDF5PCACoveragePoN(ponReader);
        final List<String> ponTargets = pon.getPanelTargetNames();
        final RealMatrix inCounts = reorderTargetsToPoNOrder(preTangentNormalized, ponTargets);
        // obtain subset of relevant targets to calculate the beta-hats;
        final int[][] betaHatTargets = new int[inCounts.getColumnDimension()][];
        for (int i = 0; i < inCounts.getColumnDimension(); i++) {
            final List<Integer> relevantTargets = new ArrayList<>();
            for (int j = 0; j < inCounts.getRowDimension(); j++) {
                if (inCounts.getEntry(j, i) > 1 + (Math.log(epsilon) / Math.log(2))) {
                    relevantTargets.add(j);
                }
            }
            betaHatTargets[i] = relevantTargets.stream().mapToInt(Integer::intValue).toArray();
        }
        // calculate beta-hats per column and check with actual values.
        final RealMatrix normalsInv = pon.getReducedPanelPInverseCounts();
        Assert.assertEquals(actual.getRowDimension(), normalsInv.getRowDimension());
        final RealMatrix normalsInvT = normalsInv.transpose();
        for (int i = 0; i < inCounts.getColumnDimension(); i++) {
            final RealMatrix inValues = inCounts.getColumnMatrix(i).transpose().getSubMatrix(new int[] { 0 }, betaHatTargets[i]);
            final RealMatrix normalValues = normalsInvT.getSubMatrix(betaHatTargets[i], IntStream.range(0, normalsInvT.getColumnDimension()).toArray());
            final RealMatrix betaHats = inValues.multiply(normalValues);
            for (int j = 0; j < actual.getRowDimension(); j++) {
                Assert.assertEquals(actual.getEntry(j, i), betaHats.getEntry(0, j), 0.000001, "Col " + i + " row " + j);
            }
        }
    }
}

Example 44 with RealMatrix

use of org.apache.commons.math3.linear.RealMatrix in project gatk by broadinstitute.

the class HDF5PCACoveragePoNCreationUtilsUnitTest method testSubtractMedianOfMedians.

@Test(dataProvider = "readCountOnlyData")
public void testSubtractMedianOfMedians(final ReadCountCollection readCounts) {
    final RealMatrix counts = readCounts.counts();
    final Median median = new Median();
    final double[] columnMedians = IntStream.range(0, counts.getColumnDimension()).mapToDouble(i -> median.evaluate(counts.getColumn(i))).toArray();
    final double center = median.evaluate(columnMedians);
    final double[][] expected = new double[counts.getRowDimension()][];
    for (int i = 0; i < expected.length; i++) {
        expected[i] = counts.getRow(i).clone();
        for (int j = 0; j < expected[i].length; j++) {
            expected[i][j] -= center;
        }
    }
    HDF5PCACoveragePoNCreationUtils.subtractMedianOfMedians(readCounts, NULL_LOGGER);
    final RealMatrix newCounts = readCounts.counts();
    Assert.assertEquals(newCounts.getColumnDimension(), expected[0].length);
    Assert.assertEquals(newCounts.getRowDimension(), expected.length);
    for (int i = 0; i < expected.length; i++) {
        for (int j = 0; j < expected[i].length; j++) {
            Assert.assertEquals(newCounts.getEntry(i, j), expected[i][j], 0.000001);
        }
    }
}

Example 45 with RealMatrix

use of org.apache.commons.math3.linear.RealMatrix in project gatk by broadinstitute.

the class HDF5PCACoveragePoNUnitTest method testReducedPoNMatrixReading.

@Test(dependsOnMethods = { "testTargetNameReading", "testLogNormalizedSampleNameReading" })
public void testReducedPoNMatrixReading() throws IOException {
    final HDF5File reader = new HDF5File(TEST_PON);
    final PCACoveragePoN pon = new HDF5PCACoveragePoN(reader);
    final List<String> targets = pon.getTargetNames();
    final List<String> samples = pon.getPanelSampleNames();
    final RealMatrix actual = pon.getReducedPanelCounts();
    Assert.assertNotNull(actual);
    Assert.assertEquals(actual.getRowDimension(), targets.size());
    Assert.assertTrue(actual.getColumnDimension() <= samples.size());
    final RealMatrix expected = readDoubleMatrix(TEST_PON_REDUCED_PON);
    MathObjectAsserts.assertRealMatrixEquals(actual, expected);
}