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

Example 51 with RealMatrix

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

the class HDF5PCACoveragePoNUnitTest method testLogNormalizedPInvMatrixReading.

@Test(dependsOnMethods = { "testTargetNameReading", "testLogNormalizedSampleNameReading" })
public void testLogNormalizedPInvMatrixReading() 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.getLogNormalizedPInverseCounts();
    Assert.assertNotNull(actual);
    Assert.assertEquals(actual.getRowDimension(), samples.size());
    Assert.assertEquals(actual.getColumnDimension(), targets.size());
    final RealMatrix expected = readDoubleMatrix(TEST_PON_LOG_NORMALS_PINV);
    MathObjectAsserts.assertRealMatrixEquals(actual, expected);
}

Example 52 with RealMatrix

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

the class RamPCACoveragePoNUnitTest method assertReducedPanelPInverseCounts.

private void assertReducedPanelPInverseCounts(final PCACoveragePoN filePoN, final PCACoveragePoN ramPoN) {
    final RealMatrix ramNormalizedCounts = ramPoN.getReducedPanelPInverseCounts();
    final RealMatrix fileNormalizedCounts = filePoN.getReducedPanelPInverseCounts();
    Assert.assertEquals(ramNormalizedCounts.subtract(fileNormalizedCounts).getNorm(), 0, 1e-9);
    ramNormalizedCounts.setEntry(3, 4, 500000);
    Assert.assertEquals(ramNormalizedCounts.getEntry(3, 4), 500000, 1e-9);
    Assert.assertNotEquals(ramPoN.getReducedPanelPInverseCounts().getEntry(3, 4), 500000, 1e-9);
    Assert.assertFalse(ramNormalizedCounts.subtract(fileNormalizedCounts).getNorm() < 1e-9);
    final RealMatrix fileNormalizedCounts2 = filePoN.getReducedPanelPInverseCounts();
    Assert.assertFalse(ramNormalizedCounts.subtract(fileNormalizedCounts2).getNorm() < 1e-9);
}

Example 53 with RealMatrix

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

the class RamPCACoveragePoNUnitTest method assertLogNormalizedPinvCounts.

private void assertLogNormalizedPinvCounts(final PCACoveragePoN filePoN, final PCACoveragePoN ramPoN) {
    final RealMatrix ramNormalizedCounts = ramPoN.getLogNormalizedPInverseCounts();
    final RealMatrix fileNormalizedCounts = filePoN.getLogNormalizedPInverseCounts();
    Assert.assertEquals(ramNormalizedCounts.subtract(fileNormalizedCounts).getNorm(), 0, 1e-9);
    ramNormalizedCounts.setEntry(3, 4, 500000);
    Assert.assertEquals(ramNormalizedCounts.getEntry(3, 4), 500000, 1e-9);
    Assert.assertNotEquals(ramPoN.getLogNormalizedPInverseCounts().getEntry(3, 4), 500000, 1e-9);
    Assert.assertFalse(ramNormalizedCounts.subtract(fileNormalizedCounts).getNorm() < 1e-9);
    final RealMatrix fileNormalizedCounts2 = filePoN.getLogNormalizedPInverseCounts();
    Assert.assertFalse(ramNormalizedCounts.subtract(fileNormalizedCounts2).getNorm() < 1e-9);
}

Example 54 with RealMatrix

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

the class RamPCACoveragePoNUnitTest method assertNormalizedCounts.

private void assertNormalizedCounts(final PCACoveragePoN filePoN, final PCACoveragePoN ramPoN) {
    final RealMatrix ramNormalizedCounts = ramPoN.getNormalizedCounts();
    final RealMatrix fileNormalizedCounts = filePoN.getNormalizedCounts();
    Assert.assertEquals(ramNormalizedCounts.subtract(fileNormalizedCounts).getNorm(), 0, 1e-9);
    ramNormalizedCounts.setEntry(3, 4, 500000);
    Assert.assertEquals(ramNormalizedCounts.getEntry(3, 4), 500000, 1e-9);
    Assert.assertNotEquals(ramPoN.getNormalizedCounts().getEntry(3, 4), 500000, 1e-9);
    Assert.assertFalse(ramNormalizedCounts.subtract(fileNormalizedCounts).getNorm() < 1e-9);
    final RealMatrix fileNormalizedCounts2 = filePoN.getNormalizedCounts();
    Assert.assertFalse(ramNormalizedCounts.subtract(fileNormalizedCounts2).getNorm() < 1e-9);
}

Example 55 with RealMatrix

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

the class HDF5LibraryUnitTest method createMatrixOfGaussianValues.

private RealMatrix createMatrixOfGaussianValues(int numRows, int numCols, final double mean, final double sigma) {
    final RealMatrix bigCounts = new Array2DRowRealMatrix(numRows, numCols);
    final RandomDataGenerator randomDataGenerator = new RandomDataGenerator();
    randomDataGenerator.reSeed(337337337);
    bigCounts.walkInOptimizedOrder(new DefaultRealMatrixChangingVisitor() {

        @Override
        public double visit(int row, int column, double value) {
            return randomDataGenerator.nextGaussian(mean, sigma);
        }
    });
    return bigCounts;
}