Package ubic.gemma.persistence.service.expression.experiment

Class RandomExperimentalDesignUtils

java.lang.Object

ubic.gemma.persistence.service.expression.experiment.RandomExperimentalDesignUtils

public class RandomExperimentalDesignUtils
extends Object

Generate random experimental design for a given experiment.

Constructor Summary

Constructors

Constructor	Description
RandomExperimentalDesignUtils()

Method Summary

Modifier and Type	Method	Description
static ExperimentalFactor	randomCategoricalFactor(ExperimentalDesign design, Collection<BioMaterial> samples, String name, int numValues)	Create and assign a categorical factor.
static ExperimentalFactor	randomCategoricalFactor(ExpressionExperiment ee, String name, int numValues)	Create and assign a categorical factor to all the samples of an experiment.
static ExperimentalFactor	randomContinuousFactor(ExperimentalDesign design, Collection<BioMaterial> samples, String name)	Create and assign a continuous factor.
static ExperimentalFactor	randomContinuousFactor(ExpressionExperiment ee, String name)	Create and assign a continuous factor to all the samples of an experiment.
ExperimentalDesign	randomExperimentalDesign(Collection<BioMaterial> samples, int numCategoricalFactors, int numContinuousFactors)	Create a random experimental design with the given number of categorical and continuous factors.
ExperimentalDesign	randomExperimentalDesign(ExpressionExperiment ee, int numCategoricalFactors, int numContinuousFactors)	Create and assign a random experimental design to the given experiment.
static void	setSeed(long seed)

Methods inherited from class java.lang.Object

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

Constructor Details

RandomExperimentalDesignUtils

public RandomExperimentalDesignUtils()

Method Details

setSeed

public static void setSeed(long seed)

randomExperimentalDesign

public ExperimentalDesign randomExperimentalDesign(ExpressionExperiment ee,
 int numCategoricalFactors,
 int numContinuousFactors)

Create and assign a random experimental design to the given experiment.

randomExperimentalDesign

public ExperimentalDesign randomExperimentalDesign(Collection<BioMaterial> samples,
 int numCategoricalFactors,
 int numContinuousFactors)

Create a random experimental design with the given number of categorical and continuous factors.

randomCategoricalFactor

public static ExperimentalFactor randomCategoricalFactor(ExpressionExperiment ee,
 String name,
 int numValues)

Create and assign a categorical factor to all the samples of an experiment.

See Also:

• randomCategoricalFactor(ExperimentalDesign, Collection, String, int)

randomCategoricalFactor

public static ExperimentalFactor randomCategoricalFactor(ExperimentalDesign design,
 Collection<BioMaterial> samples,
 String name,
 int numValues)

Create and assign a categorical factor.

Parameters:

design - design to which the factor will be added

samples - samples to which the factor values will be assigned

name - name to use for the factor

numValues - number of factor values to create

randomContinuousFactor

public static ExperimentalFactor randomContinuousFactor(ExpressionExperiment ee,
 String name)

Create and assign a continuous factor to all the samples of an experiment.

randomContinuousFactor

public static ExperimentalFactor randomContinuousFactor(ExperimentalDesign design,
 Collection<BioMaterial> samples,
 String name)

Create and assign a continuous factor.