Package ubic.gemma.persistence.service.expression.bioAssayData

Class RandomExpressionDataMatrixUtils

java.lang.Object

ubic.gemma.persistence.service.expression.bioAssayData.RandomExpressionDataMatrixUtils

public class RandomExpressionDataMatrixUtils
extends Object

Utilities for generating random ExpressionDataDoubleMatrix following various random distributions.

See Also:

RandomSingleCellDataUtils, RandomBulkDataUtils

Constructor Summary

Constructors

Constructor	Description
RandomExpressionDataMatrixUtils()

Method Summary

Modifier and Type	Method	Description
static ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix	randomCountMatrix(ubic.gemma.model.expression.experiment.ExpressionExperiment ee)	Generate a count matrix.
static ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix	randomCountMatrix(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, ubic.gemma.model.common.quantitationtype.ScaleType scaleType)	Generate a "transformed" count matrix.
static double[][]	randomExpressionMatrix(int numProbes, int numSamples, org.apache.commons.math3.distribution.IntegerDistribution distribution)	Generate a random raw expression matrix following the given discrete distribution.
static double[][]	randomExpressionMatrix(int numProbes, int numSamples, org.apache.commons.math3.distribution.RealDistribution distribution)	Generate a random raw expression matrix following the given continuous distribution.
static ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix	randomExpressionMatrix(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, ubic.gemma.model.common.quantitationtype.QuantitationType qt, List<ubic.gemma.model.expression.designElement.CompositeSequence> designElements, List<ubic.gemma.model.expression.biomaterial.BioMaterial> samples, org.apache.commons.math3.distribution.RealDistribution distribution)
static ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix	randomExpressionMatrix(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, ubic.gemma.model.common.quantitationtype.QuantitationType qt, org.apache.commons.math3.distribution.RealDistribution distribution)
static ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix	randomLinearMatrix(ubic.gemma.model.expression.experiment.ExpressionExperiment ee)
static ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix	randomLog2Matrix(ubic.gemma.model.expression.experiment.ExpressionExperiment ee)
static ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix	randomLog2Matrix(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, ubic.gemma.model.expression.bioAssayData.BioAssayDimension dimension)	Create a random matrix with a specific sample structure.
static ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix	randomLog2RatiometricMatrix(ubic.gemma.model.expression.experiment.ExpressionExperiment ee)
static void	setSeed(long seed)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

RandomExpressionDataMatrixUtils

public RandomExpressionDataMatrixUtils()

Method Detail

setSeed

public static void setSeed(long seed)

randomCountMatrix

public static ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix randomCountMatrix(ubic.gemma.model.expression.experiment.ExpressionExperiment ee)

Generate a count matrix.

The counts are drawn from a Negative Binomial distribution.

randomCountMatrix

public static ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix randomCountMatrix(ubic.gemma.model.expression.experiment.ExpressionExperiment ee,
                                                                                                ubic.gemma.model.common.quantitationtype.ScaleType scaleType)

Generate a "transformed" count matrix.

randomLinearMatrix

public static ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix randomLinearMatrix(ubic.gemma.model.expression.experiment.ExpressionExperiment ee)

randomLog2RatiometricMatrix

public static ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix randomLog2RatiometricMatrix(ubic.gemma.model.expression.experiment.ExpressionExperiment ee)

randomLog2Matrix

public static ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix randomLog2Matrix(ubic.gemma.model.expression.experiment.ExpressionExperiment ee)

randomLog2Matrix

public static ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix randomLog2Matrix(ubic.gemma.model.expression.experiment.ExpressionExperiment ee,
                                                                                               ubic.gemma.model.expression.bioAssayData.BioAssayDimension dimension)

Create a random matrix with a specific sample structure.

randomExpressionMatrix

public static ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix randomExpressionMatrix(ubic.gemma.model.expression.experiment.ExpressionExperiment ee,
                                                                                                     ubic.gemma.model.common.quantitationtype.QuantitationType qt,
                                                                                                     org.apache.commons.math3.distribution.RealDistribution distribution)

randomExpressionMatrix

public static ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix randomExpressionMatrix(ubic.gemma.model.expression.experiment.ExpressionExperiment ee,
                                                                                                     ubic.gemma.model.common.quantitationtype.QuantitationType qt,
                                                                                                     List<ubic.gemma.model.expression.designElement.CompositeSequence> designElements,
                                                                                                     List<ubic.gemma.model.expression.biomaterial.BioMaterial> samples,
                                                                                                     org.apache.commons.math3.distribution.RealDistribution distribution)

randomExpressionMatrix

public static double[][] randomExpressionMatrix(int numProbes,
                                                int numSamples,
                                                org.apache.commons.math3.distribution.RealDistribution distribution)

Generate a random raw expression matrix following the given continuous distribution.

randomExpressionMatrix

public static double[][] randomExpressionMatrix(int numProbes,
                                                int numSamples,
                                                org.apache.commons.math3.distribution.IntegerDistribution distribution)

Generate a random raw expression matrix following the given discrete distribution.