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 Details

    • DEFAULT_MODERATE_STATISTICS

      public static final boolean DEFAULT_MODERATE_STATISTICS
      Default value for whether moderated test statistics should be used.
      See Also:

  • 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

    • getAnalysisType

      public AnalysisType getAnalysisType()
      Type of analysis to perform.

    • getBaselineFactorValues

      public Map<ExperimentalFactor,FactorValue> getBaselineFactorValues()
      For each categorical factor, indicate the baseline factor value to use.

    • isModerateStatistics

      public boolean isModerateStatistics()
      Whether moderated test statistics should be used.

      This is usually done with the empirical Bayes method.

    • getFactorsToInclude

      public Set<ExperimentalFactor> getFactorsToInclude()

    • getInteractionsToInclude

      public Set<Set<ExperimentalFactor>> getInteractionsToInclude()

    • isPersist

      public boolean isPersist()
      Indicate if this analysis should be persisted.

    • getSubsetFactor

      @Nullable public ExperimentalFactor getSubsetFactor()
      Factor to subset the analysis on, if non-null.

    • getSubsetFactorValue

      @Nullable public FactorValue getSubsetFactorValue()
      If this is non-null, this is a subset analysis for this factor value.

      Only applicable for analysis on a ExpressionExperimentSubSet.

    • isIgnoreFailingSubsets

      public boolean isIgnoreFailingSubsets()
      Keep processing other subsets when encountering an AnalysisException on a subset.

      If all subset fails, an AllSubSetAnalysesFailedException will be raised which will contain individual subset failures.

    • isUseWeights

      public boolean isUseWeights()
      Set true for RNA-seq data sets

    • getFilterMode

      @Nullable public DifferentialExpressionAnalysisFilter.Mode getFilterMode()
      Override the default mode of operation for the RepetitiveValuesFilter.

    • getMinimumNumberOfAssaysToApplyFilter

      @Nullable public Integer getMinimumNumberOfAssaysToApplyFilter()
      Override the minimum number of assays to apply the repetitive value filter.
      See Also:

    • getMinimumFractionOfUniqueValues

      @Nullable public Double getMinimumFractionOfUniqueValues()
      Override the minimum number of unique values (as a fraction of the number of assays) for a particular design element to apply the filter.
      See Also:

    • isMakeArchiveFile

      public boolean isMakeArchiveFile()
      Whether to create archive files.

    • getMaxAnalysisTimeMillis

      public long getMaxAnalysisTimeMillis()
      Maximum time to spend on the analysis, in milliseconds. Ignored if zero or less.

    • setAnalysisType

      public void setAnalysisType(AnalysisType analysisType)
      Type of analysis to perform.

    • setModerateStatistics

      public void setModerateStatistics(boolean moderateStatistics)
      Whether moderated test statistics should be used.

      This is usually done with the empirical Bayes method.

    • setPersist

      public void setPersist(boolean persist)
      Indicate if this analysis should be persisted.

    • setSubsetFactor

      public void setSubsetFactor(@Nullable ExperimentalFactor subsetFactor)
      Factor to subset the analysis on, if non-null.

    • setSubsetFactorValue

      public void setSubsetFactorValue(@Nullable FactorValue subsetFactorValue)
      If this is non-null, this is a subset analysis for this factor value.

      Only applicable for analysis on a ExpressionExperimentSubSet.

    • setIgnoreFailingSubsets

      public void setIgnoreFailingSubsets(boolean ignoreFailingSubsets)
      Keep processing other subsets when encountering an AnalysisException on a subset.

      If all subset fails, an AllSubSetAnalysesFailedException will be raised which will contain individual subset failures.

    • setUseWeights

      public void setUseWeights(boolean useWeights)
      Set true for RNA-seq data sets

    • setFilterMode

      public void setFilterMode(@Nullable DifferentialExpressionAnalysisFilter.Mode filterMode)
      Override the default mode of operation for the RepetitiveValuesFilter.

    • setMinimumNumberOfAssaysToApplyFilter

      public void setMinimumNumberOfAssaysToApplyFilter(@Nullable Integer minimumNumberOfAssaysToApplyFilter)
      Override the minimum number of assays to apply the repetitive value filter.
      See Also:

    • setMinimumFractionOfUniqueValues

      public void setMinimumFractionOfUniqueValues(@Nullable Double minimumFractionOfUniqueValues)
      Override the minimum number of unique values (as a fraction of the number of assays) for a particular design element to apply the filter.
      See Also:

    • setMakeArchiveFile

      public void setMakeArchiveFile(boolean makeArchiveFile)
      Whether to create archive files.

    • setMaxAnalysisTimeMillis

      public void setMaxAnalysisTimeMillis(long maxAnalysisTimeMillis)
      Maximum time to spend on the analysis, in milliseconds. Ignored if zero or less.

    • equals

      public boolean equals(Object o)
      Overrides:
      equals in class Object

    • canEqual

      protected boolean canEqual(Object other)

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object