Package ubic.gemma.core.analysis.expression.diff

Class DifferentialExpressionAnalysisConfig

java.lang.Object

ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig

public class DifferentialExpressionAnalysisConfig
extends Object

Holds the settings used for differential expression analysis, and defines some defaults.

Author:

keshav

Field Summary

Fields

Modifier and Type	Field	Description
static final boolean	DEFAULT_MODERATE_STATISTICS	Default value for whether moderated test statistics should be used.

Constructor Summary

Constructors

Constructor	Description
DifferentialExpressionAnalysisConfig()
DifferentialExpressionAnalysisConfig(DifferentialExpressionAnalysisConfig baseConfig)	Copy constructor.

Method Summary

Modifier and Type	Method	Description
void	addBaseLineFactorValues(Map<ExperimentalFactor,FactorValue> baselineConditions)
void	addFactorsToInclude(Collection<ExperimentalFactor> factors)	Add a collection of factors to include in the analysis.
void	addInteractionsToInclude(Collection<Collection<ExperimentalFactor>> interactions)
void	addInteractionToInclude(Collection<ExperimentalFactor> factors)	Add an interaction of two factors to include in the analysis.
DifferentialExpressionAnalysis	toAnalysis()
String	toString()

Methods inherited from class java.lang.Object

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

Field Details

DEFAULT_MODERATE_STATISTICS

public static final boolean DEFAULT_MODERATE_STATISTICS

Default value for whether moderated test statistics should be used.

See Also:

• Constant Field Values

Constructor Details

DifferentialExpressionAnalysisConfig

public DifferentialExpressionAnalysisConfig()

DifferentialExpressionAnalysisConfig

public DifferentialExpressionAnalysisConfig(DifferentialExpressionAnalysisConfig baseConfig)

Copy constructor.

Method Details

addFactorsToInclude

public void addFactorsToInclude(Collection<ExperimentalFactor> factors)

Add a collection of factors to include in the analysis.

addInteractionToInclude

public void addInteractionToInclude(Collection<ExperimentalFactor> factors)

Add an interaction of two factors to include in the analysis.

addInteractionsToInclude

public void addInteractionsToInclude(Collection<Collection<ExperimentalFactor>> interactions)

addBaseLineFactorValues

public void addBaseLineFactorValues(Map<ExperimentalFactor,FactorValue> baselineConditions)

toAnalysis

public DifferentialExpressionAnalysis toAnalysis()

Returns:

representation of this analysis with populated protocol holding information from this.

toString

public String toString()

Overrides:

toString in class Object