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 booleanDEFAULT_MODERATE_STATISTICSDefault value for whether moderated test statistics should be used.
-
Constructor Summary
Constructors Constructor Description DifferentialExpressionAnalysisConfig()DifferentialExpressionAnalysisConfig(DifferentialExpressionAnalysisConfig baseConfig)Copy constructor.
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description voidaddBaseLineFactorValues(Map<ExperimentalFactor,FactorValue> baselineConditions)voidaddFactorsToInclude(Collection<ExperimentalFactor> factors)Add a collection of factors to include in the analysis.voidaddInteractionsToInclude(Collection<Collection<ExperimentalFactor>> interactions)voidaddInteractionToInclude(Collection<ExperimentalFactor> factors)Add an interaction of two factors to include in the analysis.DifferentialExpressionAnalysistoAnalysis()StringtoString()
-
-
-
Field Detail
-
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 Detail
-
DifferentialExpressionAnalysisConfig
public DifferentialExpressionAnalysisConfig()
-
DifferentialExpressionAnalysisConfig
public DifferentialExpressionAnalysisConfig(DifferentialExpressionAnalysisConfig baseConfig)
Copy constructor.
-
-
Method Detail
-
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.
-
-