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

Example 21 with RealMatrix

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

the class ReadCountCollectionUtilsUnitTest method testImputeZeroCounts.

@Test(dataProvider = "tooManyZerosData")
public void testImputeZeroCounts(final ReadCountCollection readCounts) {
    final Median median = new Median();
    final RealMatrix counts = readCounts.counts();
    final double[] targetNonZeroMedians = IntStream.range(0, counts.getRowDimension()).mapToDouble(i -> median.evaluate(DoubleStream.of(counts.getRow(i)).filter(d -> d != 0.0).toArray())).toArray();
    final double[][] expected = new double[counts.getRowDimension()][];
    final double[][] original = counts.getData();
    for (int i = 0; i < expected.length; i++) {
        final double[] rowCounts = counts.getRow(i).clone();
        expected[i] = rowCounts;
        for (int j = 0; j < expected[i].length; j++) {
            if (expected[i][j] == 0.0) {
                expected[i][j] = targetNonZeroMedians[i];
            }
        }
    }
    ReadCountCollectionUtils.imputeZeroCountsAsTargetMedians(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], "i,j == " + i + "," + j + " " + original[i][j]);
        }
    }
}

Example 22 with RealMatrix

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

the class ReadCountCollectionUtilsUnitTest method testExtremeMedianColumnsData.

@Test(dataProvider = "readCountAndPercentileData")
public void testExtremeMedianColumnsData(final ReadCountCollection readCount, final double percentile) {
    final Median median = new Median();
    final RealMatrix counts = readCount.counts();
    final double[] columnMedians = IntStream.range(0, counts.getColumnDimension()).mapToDouble(i -> median.evaluate(counts.getColumn(i))).toArray();
    final double top = new Percentile(100 - percentile).evaluate(columnMedians);
    final double bottom = new Percentile(percentile).evaluate(columnMedians);
    final Boolean[] toBeKept = DoubleStream.of(columnMedians).mapToObj(d -> d <= top && d >= bottom).toArray(Boolean[]::new);
    final int toBeKeptCount = (int) Stream.of(toBeKept).filter(b -> b).count();
    final ReadCountCollection result = ReadCountCollectionUtils.removeColumnsWithExtremeMedianCounts(readCount, percentile, NULL_LOGGER);
    Assert.assertEquals(result.columnNames().size(), toBeKeptCount);
    int nextIndex = 0;
    for (int i = 0; i < toBeKept.length; i++) {
        if (toBeKept[i]) {
            int index = result.columnNames().indexOf(readCount.columnNames().get(i));
            Assert.assertEquals(index, nextIndex++);
            Assert.assertEquals(counts.getColumn(i), result.counts().getColumn(index));
        } else {
            Assert.assertEquals(result.columnNames().indexOf(readCount.columnNames().get(i)), -1);
        }
    }
}

Example 23 with RealMatrix

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

the class SomaticGenotypingEngine method getAsRealMatrix.

//convert a likelihood matrix of alleles x reads into a RealMatrix
public static RealMatrix getAsRealMatrix(final LikelihoodMatrix<Allele> matrix) {
    final RealMatrix result = new Array2DRowRealMatrix(matrix.numberOfAlleles(), matrix.numberOfReads());
    result.walkInOptimizedOrder(new DefaultRealMatrixChangingVisitor() {

        @Override
        public double visit(int row, int column, double value) {
            return matrix.get(row, column);
        }
    });
    return result;
}

Example 24 with RealMatrix

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

the class GATKProtectedMathUtils method columnStdDevs.

/**
     * Calculates the standard deviation per column from a matrix.
     * @param matrix the input matrix.
     * @return never {@code null}, an array with as many positions as columns in {@code matrix}.
     * @throws IllegalArgumentException if {@code matrix} is {@code null}.
     */
public static double[] columnStdDevs(final RealMatrix matrix) {
    Utils.nonNull(matrix);
    final Variance varianceEvaluator = new Variance();
    return IntStream.range(0, matrix.getColumnDimension()).mapToDouble(c -> Math.sqrt(varianceEvaluator.evaluate(matrix.getColumn(c)))).toArray();
}

Example 25 with RealMatrix

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

the class GATKProtectedMathUtils method rowStdDevs.

/**
     * Calculates the standard deviation per row from a matrix.
     * @param matrix the input matrix.
     * @return never {@code null}, an array with as many positions as rows in {@code matrix}.
     * @throws IllegalArgumentException if {@code matrix} is {@code null}.
     */
public static double[] rowStdDevs(final RealMatrix matrix) {
    Utils.nonNull(matrix);
    final Variance varianceEvaluator = new Variance();
    return IntStream.range(0, matrix.getRowDimension()).mapToDouble(r -> Math.sqrt(varianceEvaluator.evaluate(matrix.getRow(r)))).toArray();
}