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	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.
protected boolean	canEqual(Object other)
boolean	equals(Object o)
AnalysisType	getAnalysisType()	Type of analysis to perform.
Set<ExperimentalFactor>	getFactorsToInclude()
Set<Set<ExperimentalFactor>>	getInteractionsToInclude()
long	getMaxAnalysisTimeMillis()	Maximum time to spend on the analysis, in milliseconds.
Double	getMinimumFractionOfUniqueValues()	Override the minimum number of unique values (as a fraction of the number of assays) for a particular design element to be included in the analysis.
Integer	getMinimumNumberOfCellsPerGene()	Override the minimum number of cells for a particular gene to be included in the analysis.
Integer	getMinimumNumberOfCellsPerSample()	Override the minimum number of cells for a particular sample to be included in the analysis.
Integer	getMinimumNumberOfSamplesToApplyRepetitiveValuesFilter()	Override the minimum number of samples to apply the repetitive value filter.
Double	getMinimumVariance()	Override the minimum variance for a particular design element to be included in the analysis.
DifferentialExpressionAnalysisFilter.RepetitiveValuesFilterMode	getRepetitiveValuesFilterMode()	Override the default mode of operation for the RepetitiveValuesFilter.
ExperimentalFactor	getSubsetFactor()	Factor to subset the analysis on, if non-null.
FactorValue	getSubsetFactorValue()	If this is non-null, this is a subset analysis for this factor value.
int	hashCode()
boolean	isIgnoreFailingSubsets()	Keep processing other subsets when encountering an AnalysisException on a subset.
boolean	isMakeArchiveFile()	Whether to create archive files.
boolean	isModerateStatistics()	Whether moderated test statistics should be used.
boolean	isPersist()	Indicate if this analysis should be persisted.
boolean	isUseWeights()	Set true for RNA-seq data sets
void	setAnalysisType(AnalysisType analysisType)	Type of analysis to perform.
void	setIgnoreFailingSubsets(boolean ignoreFailingSubsets)	Keep processing other subsets when encountering an AnalysisException on a subset.
void	setMakeArchiveFile(boolean makeArchiveFile)	Whether to create archive files.
void	setMaxAnalysisTimeMillis(long maxAnalysisTimeMillis)	Maximum time to spend on the analysis, in milliseconds.
void	setMinimumFractionOfUniqueValues(Double minimumFractionOfUniqueValues)	Override the minimum number of unique values (as a fraction of the number of assays) for a particular design element to be included in the analysis.
void	setMinimumNumberOfCellsPerGene(Integer minimumNumberOfCellsPerGene)	Override the minimum number of cells for a particular gene to be included in the analysis.
void	setMinimumNumberOfCellsPerSample(Integer minimumNumberOfCellsPerSample)	Override the minimum number of cells for a particular sample to be included in the analysis.
void	setMinimumNumberOfSamplesToApplyRepetitiveValuesFilter(Integer minimumNumberOfSamplesToApplyRepetitiveValuesFilter)	Override the minimum number of samples to apply the repetitive value filter.
void	setMinimumVariance(Double minimumVariance)	Override the minimum variance for a particular design element to be included in the analysis.
void	setModerateStatistics(boolean moderateStatistics)	Whether moderated test statistics should be used.
void	setPersist(boolean persist)	Indicate if this analysis should be persisted.
void	setRepetitiveValuesFilterMode(DifferentialExpressionAnalysisFilter.RepetitiveValuesFilterMode repetitiveValuesFilterMode)	Override the default mode of operation for the RepetitiveValuesFilter.
void	setSubsetFactor(ExperimentalFactor subsetFactor)	Factor to subset the analysis on, if non-null.
void	setSubsetFactorValue(FactorValue subsetFactorValue)	If this is non-null, this is a subset analysis for this factor value.
void	setUseWeights(boolean useWeights)	Set true for RNA-seq data sets
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, 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)

getAnalysisType

public AnalysisType getAnalysisType()

Type of analysis to perform.

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

getMinimumNumberOfCellsPerSample

@Nullable
public Integer getMinimumNumberOfCellsPerSample()

Override the minimum number of cells for a particular sample to be included in the analysis.

This is only applied if ExpressionDataDoubleMatrix.getNumberOfCells() or BioAssay.getNumberOfCells() is populated. Note that the BioAssay-level number of cells is only considered for preferred QTs.

Defaults to DifferentialExpressionAnalysisFilter.DEFAULT_MINIMUM_NUMBER_OF_CELLS_PER_SAMPLE.

getMinimumNumberOfCellsPerGene

@Nullable
public Integer getMinimumNumberOfCellsPerGene()

Override the minimum number of cells for a particular gene to be included in the analysis.

This is only applied if ExpressionDataDoubleMatrix.getNumberOfCells() is populated.

Defaults to DifferentialExpressionAnalysisFilter.DEFAULT_MINIMUM_NUMBER_OF_CELLS_PER_GENE.

getRepetitiveValuesFilterMode

@Nullable
public DifferentialExpressionAnalysisFilter.RepetitiveValuesFilterMode getRepetitiveValuesFilterMode()

Override the default mode of operation for the RepetitiveValuesFilter.

Defaults to DifferentialExpressionAnalysisFilter.DEFAULT_REPETITIVE_VALUES_FILTER_MODE

getMinimumNumberOfSamplesToApplyRepetitiveValuesFilter

@Nullable
public Integer getMinimumNumberOfSamplesToApplyRepetitiveValuesFilter()

Override the minimum number of samples to apply the repetitive value filter.

Defaults to DifferentialExpressionAnalysisFilter.DEFAULT_MINIMUM_NUMBER_OF_SAMPLES_TO_APPLY_REPETITIVE_VALUES_FILTER

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 be included in the analysis.

Defaults to DifferentialExpressionAnalysisFilter.DEFAULT_MINIMUM_FRACTION_OF_UNIQUE_VALUES.

getMinimumVariance

@Nullable
public Double getMinimumVariance()

Override the minimum variance for a particular design element to be included in the analysis.

Defaults to DifferentialExpressionAnalysisFilter.DEFAULT_MINIMUM_VARIANCE.

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

setMinimumNumberOfCellsPerSample

public void setMinimumNumberOfCellsPerSample(@Nullable
 Integer minimumNumberOfCellsPerSample)

Override the minimum number of cells for a particular sample to be included in the analysis.

This is only applied if ExpressionDataDoubleMatrix.getNumberOfCells() or BioAssay.getNumberOfCells() is populated. Note that the BioAssay-level number of cells is only considered for preferred QTs.

Defaults to DifferentialExpressionAnalysisFilter.DEFAULT_MINIMUM_NUMBER_OF_CELLS_PER_SAMPLE.

setMinimumNumberOfCellsPerGene

public void setMinimumNumberOfCellsPerGene(@Nullable
 Integer minimumNumberOfCellsPerGene)

Override the minimum number of cells for a particular gene to be included in the analysis.

This is only applied if ExpressionDataDoubleMatrix.getNumberOfCells() is populated.

Defaults to DifferentialExpressionAnalysisFilter.DEFAULT_MINIMUM_NUMBER_OF_CELLS_PER_GENE.

setRepetitiveValuesFilterMode

public void setRepetitiveValuesFilterMode(@Nullable
 DifferentialExpressionAnalysisFilter.RepetitiveValuesFilterMode repetitiveValuesFilterMode)

Override the default mode of operation for the RepetitiveValuesFilter.

Defaults to DifferentialExpressionAnalysisFilter.DEFAULT_REPETITIVE_VALUES_FILTER_MODE

setMinimumNumberOfSamplesToApplyRepetitiveValuesFilter

public void setMinimumNumberOfSamplesToApplyRepetitiveValuesFilter(@Nullable
 Integer minimumNumberOfSamplesToApplyRepetitiveValuesFilter)

Override the minimum number of samples to apply the repetitive value filter.

Defaults to DifferentialExpressionAnalysisFilter.DEFAULT_MINIMUM_NUMBER_OF_SAMPLES_TO_APPLY_REPETITIVE_VALUES_FILTER

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 be included in the analysis.

Defaults to DifferentialExpressionAnalysisFilter.DEFAULT_MINIMUM_FRACTION_OF_UNIQUE_VALUES.

setMinimumVariance

public void setMinimumVariance(@Nullable
 Double minimumVariance)

Override the minimum variance for a particular design element to be included in the analysis.

Defaults to DifferentialExpressionAnalysisFilter.DEFAULT_MINIMUM_VARIANCE.

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

toString

public String toString()

Overrides:

toString in class Object