Examples with DoubleMatrix2D cern.colt.matrix.DoubleMatrix2D used on opensource projects

Example 51 with DoubleMatrix2D

use of cern.colt.matrix.DoubleMatrix2D in project Gemma by PavlidisLab.

the class ComBat method computeDesignMatrix.

/**
 * ComBat parameterizes the model without an intercept, instead using all possible columns for batch (what the heck
 * do you call this parameterization?) This is important. Each batch has its own parameter.
 *
 * @return double matrix 2d
 */
private DoubleMatrix2D computeDesignMatrix() {
    DoubleMatrix2D design;
    /*
         * Find the batch
         */
    DesignMatrix d = null;
    int batchFactorColumnIndex = sampleInfo.getColIndexByName(ComBat.BATCH_COLUMN_NAME);
    Object[] batchFactor = sampleInfo.getColumn(batchFactorColumnIndex);
    if (batchFactor != null) {
        d = new DesignMatrix(batchFactor, 1, ComBat.BATCH_COLUMN_NAME);
    }
    if (d == null) {
        throw new IllegalStateException("No batch factor was found");
    }
    ObjectMatrix<String, String, Object> sampleInfoWithoutBatchFactor = this.getSampleInfoWithoutBatchFactor(batchFactorColumnIndex);
    d.add(sampleInfoWithoutBatchFactor);
    design = d.getDoubleMatrix();
    return design;
}

Example 52 with DoubleMatrix2D

use of cern.colt.matrix.DoubleMatrix2D in project Gemma by PavlidisLab.

the class ComBat method runParametric.

private void runParametric(final DoubleMatrix2D sdata, DoubleMatrix2D gammastar, DoubleMatrix2D deltastar) {
    int batchIndex = 0;
    for (String batchId : batches.keySet()) {
        DoubleMatrix2D batchData = this.getBatchData(sdata, batchId);
        DoubleMatrix1D[] batchResults;
        batchResults = this.itSol(batchData, gammaHat.viewRow(batchIndex), deltaHat.viewRow(batchIndex), gammaBar.get(batchIndex), t2.get(batchIndex), aPrior.get(batchIndex), bPrior.get(batchIndex));
        for (int j = 0; j < batchResults[0].size(); j++) {
            gammastar.set(batchIndex, j, batchResults[0].get(j));
        }
        for (int j = 0; j < batchResults[1].size(); j++) {
            deltastar.set(batchIndex, j, batchResults[1].get(j));
        }
        batchIndex++;
    }
}

Example 53 with DoubleMatrix2D

use of cern.colt.matrix.DoubleMatrix2D in project Gemma by PavlidisLab.

the class ComBat method stepSum.

private DoubleMatrix1D stepSum(DoubleMatrix2D matrix, DoubleMatrix1D gnew) {
    Algebra s = new Algebra();
    DoubleMatrix2D g = new DenseDoubleMatrix2D(1, gnew.size());
    for (int i = 0; i < gnew.size(); i++) {
        g.set(0, i, gnew.get(i));
    }
    DoubleMatrix2D a = new DenseDoubleMatrix2D(1, matrix.columns());
    a.assign(1.0);
    /*
         * subtract column gnew from each column of data; square; then sum over each row.
         */
    DoubleMatrix2D deltas = matrix.copy().assign((s.mult(s.transpose(g), a)), Functions.minus).assign(Functions.square);
    DoubleMatrix1D sumsq = new DenseDoubleMatrix1D(deltas.rows());
    sumsq.assign(0.0);
    for (int i = 0; i < deltas.rows(); i++) {
        sumsq.set(i, DescriptiveWithMissing.sum(new DoubleArrayList(deltas.viewRow(i).toArray())));
    }
    return sumsq;
}

Example 54 with DoubleMatrix2D

use of cern.colt.matrix.DoubleMatrix2D in project Gemma by PavlidisLab.

the class ComBat method runNonParametric.

private void runNonParametric(final DoubleMatrix2D sdata, DoubleMatrix2D gammastar, DoubleMatrix2D deltastar) {
    final ConcurrentHashMap<String, DoubleMatrix1D[]> results = new ConcurrentHashMap<>();
    int numThreads = Math.min(batches.size(), Runtime.getRuntime().availableProcessors());
    ComBat.log.info("Runing nonparametric estimation on " + numThreads + " threads");
    Future<?>[] futures = new Future[numThreads];
    ExecutorService service = Executors.newCachedThreadPool();
    /*
         * Divvy up batches over threads.
         */
    int batchesPerThread = batches.size() / numThreads;
    final String[] batchIds = batches.keySet().toArray(new String[] {});
    for (int i = 0; i < numThreads; i++) {
        final int firstBatch = i * batchesPerThread;
        final int lastBatch = i == (numThreads - 1) ? batches.size() : firstBatch + batchesPerThread;
        futures[i] = service.submit(new Runnable() {

            @Override
            public void run() {
                for (int k = firstBatch; k < lastBatch; k++) {
                    String batchId = batchIds[k];
                    DoubleMatrix2D batchData = ComBat.this.getBatchData(sdata, batchId);
                    DoubleMatrix1D[] batchResults = ComBat.this.nonParametricFit(batchData, gammaHat.viewRow(k), deltaHat.viewRow(k));
                    results.put(batchId, batchResults);
                }
            }
        });
    }
    service.shutdown();
    boolean allDone = false;
    do {
        for (Future<?> f : futures) {
            allDone = true;
            if (!f.isDone() && !f.isCancelled()) {
                allDone = false;
                break;
            }
        }
    } while (!allDone);
    for (int i = 0; i < batchIds.length; i++) {
        String batchId = batchIds[i];
        DoubleMatrix1D[] batchResults = results.get(batchId);
        for (int j = 0; j < batchResults[0].size(); j++) {
            gammastar.set(i, j, batchResults[0].get(j));
        }
        for (int j = 0; j < batchResults[1].size(); j++) {
            deltastar.set(i, j, batchResults[1].get(j));
        }
    }
}

Example 55 with DoubleMatrix2D

use of cern.colt.matrix.DoubleMatrix2D in project Gemma by PavlidisLab.

the class ComBat method gammaHat.

private void gammaHat(DoubleMatrix2D sdata) {
    DoubleMatrix2D Xb = x.viewPart(0, 0, x.rows(), numBatches);
    gammaHat = new LeastSquaresFit(Xb, sdata).getCoefficients();
}