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

Class DifferentialExpressionAnalysisConfig

  • All Implemented Interfaces:
    Serializable
    public class DifferentialExpressionAnalysisConfig
extends Object
implements Serializable
    Holds the settings used for differential expression analysis, and defines some defaults.
    Author:
    keshav
    See Also:
    Serialized Form

    • Field Detail

      • DEFAULT_EBAYES

        public static final boolean DEFAULT_EBAYES
        Default value for whether empirical Bayes moderation of test statistics should be used.
        See Also:
        Constant Field Values

    • Constructor Detail

      • DifferentialExpressionAnalysisConfig

        public DifferentialExpressionAnalysisConfig()

    • Method Detail

      • addInteractionToInclude

        public void addInteractionToInclude​(ExperimentalFactor... factors)

      • setBaseLineFactorValues

        public void setBaseLineFactorValues​(Map<ExperimentalFactor,​FactorValue> baseLineFactorValues)
        Parameters:
        baseLineFactorValues - the baseLineFactorValues to set

      • setFactorsToInclude

        public void setFactorsToInclude​(List<ExperimentalFactor> factorsToInclude)
        Parameters:
        factorsToInclude - the factorsToInclude to set

      • setInteractionsToInclude

        public void setInteractionsToInclude​(Collection<Collection<ExperimentalFactor>> interactionsToInclude)
        Parameters:
        interactionsToInclude - the interactionsToInclude to set

      • getModerateStatistics

        public boolean getModerateStatistics()
        Returns:
        true if empirical Bayes moderated test statisics should be used

      • setModerateStatistics

        public void setModerateStatistics​(boolean ebayes)

      • getPersist

        public boolean getPersist()

      • setPersist

        public void setPersist​(boolean persist)

      • setSubsetFactor

        public void setSubsetFactor​(ExperimentalFactor subsetFactor)
        Parameters:
        subsetFactor - the subsetFactor to set

      • getSubsetFactorValue

        public FactorValue getSubsetFactorValue()

      • setSubsetFactorValue

        public void setSubsetFactorValue​(FactorValue subsetFactorValue)

      • getUseWeights

        public boolean getUseWeights()

      • setUseWeights

        public void setUseWeights​(boolean weighted)

      • toAnalysis

        public DifferentialExpressionAnalysis toAnalysis()
        Returns:
        representation of this analysis with populated protocol holding information from this.

      • getMakeArchiveFile

        public boolean getMakeArchiveFile()

      • setMakeArchiveFile

        public void setMakeArchiveFile​(boolean makeArchiveFile)