Uses of Class
ubic.gemma.model.expression.experiment.ExperimentalFactor

Packages that use ExperimentalFactor

Package	Description
ubic.gemma.cli.util
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.analysis.preprocess	This package contains classes for preprocessing expression data.
ubic.gemma.core.analysis.preprocess.batcheffects
ubic.gemma.core.analysis.preprocess.svd
ubic.gemma.core.analysis.singleCell	This package contains classes for analysing single-cell expression data.
ubic.gemma.core.analysis.singleCell.aggregate	This package contains classes for subsetting and aggregating single-cell data.
ubic.gemma.core.datastructure.matrix	This package contains data structures for representing matrices of gene expression.
ubic.gemma.core.datastructure.matrix.io	This package contains I/O utilities for reading and writing expression data matrices.
ubic.gemma.core.loader.expression	This package contains interfaces and classes for loading expression data.
ubic.gemma.core.loader.expression.singleCell	This package contains classes for loading single-cell expression data.
ubic.gemma.core.tasks.analysis.diffex
ubic.gemma.core.visualization
ubic.gemma.core.visualization.cellbrowser	This package contains classes related to the Cell Browser visualization tool.
ubic.gemma.model.analysis.expression
ubic.gemma.model.analysis.expression.diff
ubic.gemma.model.expression.experiment
ubic.gemma.persistence.service.analysis.expression.diff
ubic.gemma.persistence.service.expression.biomaterial
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.util
ubic.gemma.web.controller.expression.experiment
ubic.gemma.web.controller.visualization

Uses of ExperimentalFactor in ubic.gemma.cli.util

Methods in ubic.gemma.cli.util that return ExperimentalFactor

Modifier and Type	Method	Description
ExperimentalFactor	EntityLocator.locateExperimentalFactor(ExpressionExperiment expressionExperiment, String ctfName)
ExperimentalFactor	EntityLocatorImpl.locateExperimentalFactor(ExpressionExperiment expressionExperiment, String identifier)

Uses of ExperimentalFactor in ubic.gemma.core.analysis.expression.diff

Methods in ubic.gemma.core.analysis.expression.diff that return ExperimentalFactor

Modifier and Type	Method	Description
ExperimentalFactor	DifferentialExpressionAnalysisConfig.getSubsetFactor()	Factor to subset the analysis on, if non-null.

Methods in ubic.gemma.core.analysis.expression.diff that return types with arguments of type ExperimentalFactor

Modifier and Type	Method	Description
static ObjectMatrix<BioMaterial,ExperimentalFactor,Object>	DiffExAnalyzerUtils.buildDesignMatrix(List<ExperimentalFactor> factors, List<BioMaterial> samplesUsed, boolean allowMissingValues)	Build a design matrix for the given factors and samples.
static Map<ExperimentalFactor,FactorValue>	BaselineSelection.getBaselineConditions(List<BioMaterial> samplesUsed, List<ExperimentalFactor> factors)
Map<ExperimentalFactor,FactorValue>	DifferentialExpressionAnalysisConfig.getBaselineFactorValues()	For each categorical factor, indicate the baseline factor value to use.
static Map<ExperimentalFactor,FactorValue>	BaselineSelection.getBaselineLevels(Collection<ExperimentalFactor> factors)	Identify the FactorValue that should be treated as 'Baseline' for each of the given factors.
static Map<ExperimentalFactor,FactorValue>	BaselineSelection.getBaselineLevels(Collection<ExperimentalFactor> factors, List<BioMaterial> samplesUsed)	Identify the FactorValue that should be treated as 'Baseline' for each of the given factors.
Set<ExperimentalFactor>	DifferentialExpressionAnalysisConfig.getFactorsToInclude()
Set<Set<ExperimentalFactor>>	DifferentialExpressionAnalysisConfig.getInteractionsToInclude()

Methods in ubic.gemma.core.analysis.expression.diff with parameters of type ExperimentalFactor

Modifier and Type	Method	Description
static boolean	DifferentialExpressionAnalysisUtil.checkValidForLm(BioAssaySet expressionExperiment, ExperimentalFactor experimentalFactor)	Check that the factorValues are measurements, or that there are at least two assays for at least one factor value.
ExperimentalFactorValueObject	GeneDifferentialExpressionService.configExperimentalFactorValueObject(ExperimentalFactor ef)
ExperimentalFactorValueObject	GeneDifferentialExpressionServiceImpl.configExperimentalFactorValueObject(ExperimentalFactor ef)
static AnalysisType	DiffExAnalyzerUtils.determineAnalysisType(BioAssaySet bioAssaySet, Collection<ExperimentalFactor> experimentalFactors, ExperimentalFactor subsetFactor, boolean includeInteractionsIfPossible)	Determines the analysis to execute based on the experimental factors, factor values, and block design.
static String	DiffExAnalyzerUtils.nameForR(ExperimentalFactor experimentalFactor)	Create a name for the factor that is suitable for R.
static void	DiffExAnalyzerUtils.populateFactorValuesFromBASet(BioAssaySet ee, ExperimentalFactor f, Collection<FactorValue> fvs)
void	DifferentialExpressionAnalysisConfig.setSubsetFactor(ExperimentalFactor subsetFactor)	Factor to subset the analysis on, if non-null.

Method parameters in ubic.gemma.core.analysis.expression.diff with type arguments of type ExperimentalFactor

Modifier and Type	Method	Description
void	DifferentialExpressionAnalysisConfig.addBaseLineFactorValues(Map<ExperimentalFactor,FactorValue> baselineConditions)
void	DifferentialExpressionAnalysisConfig.addFactorsToInclude(Collection<ExperimentalFactor> factors)	Add a collection of factors to include in the analysis.
void	DifferentialExpressionAnalysisConfig.addInteractionsToInclude(Collection<Collection<ExperimentalFactor>> interactions)
void	DifferentialExpressionAnalysisConfig.addInteractionToInclude(Collection<ExperimentalFactor> factors)	Add an interaction of two factors to include in the analysis.
static boolean	DifferentialExpressionAnalysisUtil.blockComplete(BioAssaySet expressionExperiment, Collection<ExperimentalFactor> factors)	Returns true if the block design is complete and there are at least 2 biological replicates for each "group", false otherwise.
static ObjectMatrix<BioMaterial,ExperimentalFactor,Object>	DiffExAnalyzerUtils.buildDesignMatrix(List<ExperimentalFactor> factors, List<BioMaterial> samplesUsed, boolean allowMissingValues)	Build a design matrix for the given factors and samples.
static ObjectMatrix<String,String,Object>	DiffExAnalyzerUtils.buildRDesignMatrix(List<ExperimentalFactor> factors, List<BioMaterial> samplesUsed, boolean allowMissingValues)	Build an R-friendly design matrix.
static ObjectMatrix<String,String,Object>	DiffExAnalyzerUtils.buildRDesignMatrix(List<ExperimentalFactor> factors, List<BioMaterial> samplesUsed, Map<ExperimentalFactor,FactorValue> baselines, boolean allowMissingValues)	A variant of DiffExAnalyzerUtils.buildRDesignMatrix(List, List, boolean) that allows for reusing baselines for repeated calls.
static ObjectMatrix<String,String,Object>	DiffExAnalyzerUtils.buildRDesignMatrix(List<ExperimentalFactor> factors, List<BioMaterial> samplesUsed, Map<ExperimentalFactor,FactorValue> baselines, boolean allowMissingValues)	A variant of DiffExAnalyzerUtils.buildRDesignMatrix(List, List, boolean) that allows for reusing baselines for repeated calls.
static AnalysisType	DiffExAnalyzerUtils.determineAnalysisType(BioAssaySet bioAssaySet, Collection<ExperimentalFactor> experimentalFactors, ExperimentalFactor subsetFactor, boolean includeInteractionsIfPossible)	Determines the analysis to execute based on the experimental factors, factor values, and block design.
static String	DiffExAnalyzerUtils.formatInteraction(Set<ExperimentalFactor> i)	Format an interaction of factors.
static Map<ExperimentalFactor,FactorValue>	BaselineSelection.getBaselineLevels(Collection<ExperimentalFactor> factors)	Identify the FactorValue that should be treated as 'Baseline' for each of the given factors.
static Map<ExperimentalFactor,FactorValue>	BaselineSelection.getBaselineLevels(Collection<ExperimentalFactor> factors, List<BioMaterial> samplesUsed)	Identify the FactorValue that should be treated as 'Baseline' for each of the given factors.

Uses of ExperimentalFactor in ubic.gemma.core.analysis.preprocess

Methods in ubic.gemma.core.analysis.preprocess with parameters of type ExperimentalFactor

Modifier and Type	Method	Description
ExpressionExperimentSet	SplitExperimentService.split(ExpressionExperiment expressionExperiment, ExperimentalFactor splitOn, boolean postProcess)	Split an experiment into multiple experiments based on a factor.
ExpressionExperimentSet	SplitExperimentServiceImpl.split(ExpressionExperiment toSplit, ExperimentalFactor splitOn, boolean postProcess)

Uses of ExperimentalFactor in ubic.gemma.core.analysis.preprocess.batcheffects

Methods in ubic.gemma.core.analysis.preprocess.batcheffects that return ExperimentalFactor

Modifier and Type	Method	Description
ExperimentalFactor	BatchInfoPopulationHelperService.createBatchFactor(ExpressionExperiment ee, Map<BioMaterial,Date> dates)
ExperimentalFactor	BatchInfoPopulationHelperServiceImpl.createBatchFactor(ExpressionExperiment ee, Map<BioMaterial,Date> dates)
ExperimentalFactor	BatchInfoPopulationHelperService.createRnaSeqBatchFactor(ExpressionExperiment ee, Map<BioMaterial,String> headers)	For RNA-seq, we based the batching on the available device/run/flowcell/lane information
ExperimentalFactor	BatchInfoPopulationHelperServiceImpl.createRnaSeqBatchFactor(ExpressionExperiment ee, Map<BioMaterial,String> headers)
ExperimentalFactor	ExpressionExperimentBatchCorrectionService.getBatchFactor(ExpressionExperiment ee)	For convenience of some testing classes
ExperimentalFactor	ExpressionExperimentBatchCorrectionServiceImpl.getBatchFactor(ExpressionExperiment ee)
ExperimentalFactor	BatchConfound.getFactor()	Factor being confounded with the batches.

Constructors in ubic.gemma.core.analysis.preprocess.batcheffects with parameters of type ExperimentalFactor

Modifier	Constructor	Description
	BatchConfound(BioAssaySet bioAssaySet, ExperimentalFactor factor, double chiSquare, int df, double pValue, int numBatches)	Creates a new BatchConfound instance.

Uses of ExperimentalFactor in ubic.gemma.core.analysis.preprocess.svd

Methods in ubic.gemma.core.analysis.preprocess.svd that return types with arguments of type ExperimentalFactor

Modifier and Type	Method	Description
Map<Integer,Map<ExperimentalFactor,Double>>	SVDResult.getFactorCorrelations()	Map of component to a map of ExperimentalFactor IDs to correlations of that factor with the component.
Map<Integer,Map<ExperimentalFactor,Double>>	SVDResult.getFactorPVals()	Map of component to map of ExperimentalFactor IDs to P-values for the association of that factor with the component.
Map<ExperimentalFactor,List<Number>>	SVDResult.getFactors()	Map of factors to the double-ized representations of them.
Set<ExperimentalFactor>	SVDService.getImportantFactors(ExpressionExperiment ee, Collection<ExperimentalFactor> experimentalFactors, Double importanceThreshold)
Set<ExperimentalFactor>	SVDServiceImpl.getImportantFactors(ExpressionExperiment ee, Collection<ExperimentalFactor> experimentalFactors, Double importanceThreshold)

Method parameters in ubic.gemma.core.analysis.preprocess.svd with type arguments of type ExperimentalFactor

Modifier and Type	Method	Description
Set<ExperimentalFactor>	SVDService.getImportantFactors(ExpressionExperiment ee, Collection<ExperimentalFactor> experimentalFactors, Double importanceThreshold)
Set<ExperimentalFactor>	SVDServiceImpl.getImportantFactors(ExpressionExperiment ee, Collection<ExperimentalFactor> experimentalFactors, Double importanceThreshold)
static void	SVDServiceImpl.populateBMFMap(Map<ExperimentalFactor,Map<BioMaterial,Number>> bioMaterialFactorMap, BioMaterial bm)	Retrieve relationships between factors, biomaterials and factor values.

Uses of ExperimentalFactor in ubic.gemma.core.analysis.singleCell

Methods in ubic.gemma.core.analysis.singleCell with parameters of type ExperimentalFactor

Modifier and Type	Method	Description
static Map<Characteristic,FactorValue>	CellLevelCharacteristicsMappingUtils.createMappingByFactorValueCharacteristics(CellLevelCharacteristics cta, ExperimentalFactor factor)	Map the cell types from a cell type assignment to factor values in a cell type factor.
static Map<Characteristic,FactorValue>	CellLevelCharacteristicsMappingUtils.createMappingBySubSetCharacteristics(CellLevelCharacteristics clc, ExperimentalFactor factor, Map<FactorValue,ExpressionExperimentSubSet> subsets)	Infer the mapping of cell type assignments to factor values using a subset structure.
static Map<Characteristic,FactorValue>	CellLevelCharacteristicsMappingUtils.readMappingFromFile(CellLevelCharacteristics clc, ExperimentalFactor factor, Path cellTypeMappingFile)	Create a mapping of cell type assignments to factor values from a file.
static void	CellLevelCharacteristicsMappingUtils.writeMapping(CellLevelCharacteristics cta, ExperimentalFactor factor, Map<Characteristic,FactorValue> cta2f, Writer dest)	Create a mapping of cell type assignments to factor values from a file.

Uses of ExperimentalFactor in ubic.gemma.core.analysis.singleCell.aggregate

Methods in ubic.gemma.core.analysis.singleCell.aggregate with parameters of type ExperimentalFactor

Modifier and Type	Method	Description
QuantitationType	SingleCellExpressionExperimentAggregateService.aggregateVectors(ExpressionExperiment ee, QuantitationType qt, List<BioAssay> cellBAs, CellLevelCharacteristics cellLevelCharacteristics, ExperimentalFactor factor, Map<Characteristic,FactorValue> cellTypeMapping, SingleCellAggregationConfig config)	Aggregate preferred single-cell data vectors by the given cell-level characteristics.
QuantitationType	SingleCellExpressionExperimentAggregateServiceImpl.aggregateVectors(ExpressionExperiment ee, QuantitationType qt, List<BioAssay> cellBAs, CellLevelCharacteristics cellLevelCharacteristics, ExperimentalFactor factor, Map<Characteristic,FactorValue> cellType2Factor, SingleCellAggregationConfig config)
List<ExpressionExperimentSubSet>	SingleCellExpressionExperimentSubSetService.createSubSets(ExpressionExperiment ee, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic,FactorValue> cellTypeMapping, SingleCellExperimentSubSetsCreationConfig config)	Subset biomaterials and bioassays by the given CellLevelCharacteristics.
List<ExpressionExperimentSubSet>	SingleCellExpressionExperimentSubSetServiceImpl.createSubSets(ExpressionExperiment ee, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic,FactorValue> mappedCellTypeFactors, SingleCellExperimentSubSetsCreationConfig config)
QuantitationType	SingleCellExpressionExperimentCreateSubSetsAndAggregateService.createSubSetsAndAggregate(ExpressionExperiment expressionExperiment, QuantitationType scQt, CellLevelCharacteristics cta, ExperimentalFactor cellTypeFactor, Map<Characteristic,FactorValue> c2f, SingleCellExperimentSubSetsCreationConfig singleCellExperimentSubSetsCreationConfig, SingleCellAggregationConfig config)	Create subsets and aggregate by any cell-level characteristics.
QuantitationType	SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceImpl.createSubSetsAndAggregate(ExpressionExperiment expressionExperiment, QuantitationType scQt, CellLevelCharacteristics clc, ExperimentalFactor cellTypeFactor, Map<Characteristic,FactorValue> c2f, SingleCellExperimentSubSetsCreationConfig singleCellExperimentSubSetsCreationConfig, SingleCellAggregationConfig config)
QuantitationType	SingleCellExpressionExperimentCreateSubSetsAndAggregateService.redoAggregate(ExpressionExperiment expressionExperiment, QuantitationType scQt, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic,FactorValue> c2f, BioAssayDimension dimension, QuantitationType previousQt, SingleCellAggregationConfig config)	Re-aggregate a dataset by any cell-level characteristics.
QuantitationType	SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceImpl.redoAggregate(ExpressionExperiment expressionExperiment, QuantitationType scQt, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic,FactorValue> c2f, BioAssayDimension dimension, QuantitationType previousQt, SingleCellAggregationConfig config)

Uses of ExperimentalFactor in ubic.gemma.core.datastructure.matrix

Methods in ubic.gemma.core.datastructure.matrix with parameters of type ExperimentalFactor

Modifier and Type	Method	Description
static List<BioMaterial>	ExpressionDataMatrixColumnSort.orderByExperimentalDesign(List<BioMaterial> start, Collection<ExperimentalFactor> factors, ExperimentalFactor primaryFactor)
static <R> DoubleMatrix<R,BioAssay>	ExpressionDataMatrixColumnSort.orderByExperimentalDesign(DoubleMatrix<R,BioAssay> mat, Collection<ExperimentalFactor> factors, ExperimentalFactor primaryFactor)
static List<BioMaterial>	ExpressionDataMatrixColumnSort.orderByExperimentalDesign(BulkExpressionDataMatrix<?> dmatrix, Collection<ExperimentalFactor> factors, ExperimentalFactor primaryFactor)

Method parameters in ubic.gemma.core.datastructure.matrix with type arguments of type ExperimentalFactor

Modifier and Type	Method	Description
static List<BioMaterial>	ExpressionDataMatrixColumnSort.orderByExperimentalDesign(List<BioMaterial> start, Collection<ExperimentalFactor> factors, ExperimentalFactor primaryFactor)
static <R> DoubleMatrix<R,BioAssay>	ExpressionDataMatrixColumnSort.orderByExperimentalDesign(DoubleMatrix<R,BioAssay> mat, Collection<ExperimentalFactor> factors, ExperimentalFactor primaryFactor)
static List<BioMaterial>	ExpressionDataMatrixColumnSort.orderByExperimentalDesign(BulkExpressionDataMatrix<?> dmatrix, Collection<ExperimentalFactor> factors, ExperimentalFactor primaryFactor)

Uses of ExperimentalFactor in ubic.gemma.core.datastructure.matrix.io

Methods in ubic.gemma.core.datastructure.matrix.io with parameters of type ExperimentalFactor

Modifier and Type	Method	Description
static String	ExpressionDataWriterUtils.constructExperimentalFactorName(ExperimentalFactor ef)	Construct an ExperimentalFactor column name.

Method parameters in ubic.gemma.core.datastructure.matrix.io with type arguments of type ExperimentalFactor

Modifier and Type	Method	Description
static String[]	ExpressionDataWriterUtils.constructExperimentalFactorNames(List<ExperimentalFactor> factors)	Construct an ExperimentalFactor column names for a list of factors.

Uses of ExperimentalFactor in ubic.gemma.core.loader.expression

Methods in ubic.gemma.core.loader.expression that return types with arguments of type ExperimentalFactor

Modifier and Type	Method	Description
Set<ExperimentalFactor>	AbstractDelegatingDataLoader.getFactors(Collection<BioAssay> samples, Map<BioMaterial,Set<FactorValue>> factorValueAssignments)
Set<ExperimentalFactor>	DataLoader.getFactors(Collection<BioAssay> samples, Map<BioMaterial,Set<FactorValue>> factorValueAssignments)	Load experimental factors present in the data.

Uses of ExperimentalFactor in ubic.gemma.core.loader.expression.singleCell

Methods in ubic.gemma.core.loader.expression.singleCell that return types with arguments of type ExperimentalFactor

Modifier and Type	Method	Description
Set<ExperimentalFactor>	AnnDataSingleCellDataLoader.getFactors(Collection<BioAssay> samples, Map<BioMaterial,Set<FactorValue>> factorValueAssignments)
Set<ExperimentalFactor>	MexSingleCellDataLoader.getFactors(Collection<BioAssay> samples, Map<BioMaterial,Set<FactorValue>> factorValueAssignments)	MEX does not provide experimental factors.
Set<ExperimentalFactor>	NullSingleCellDataLoader.getFactors(Collection<BioAssay> samples, Map<BioMaterial,Set<FactorValue>> factorValueAssignments)

Uses of ExperimentalFactor in ubic.gemma.core.tasks.analysis.diffex

Methods in ubic.gemma.core.tasks.analysis.diffex that return ExperimentalFactor

Modifier and Type	Method	Description
ExperimentalFactor	DifferentialExpressionAnalysisTaskCommand.getSubsetFactor()

Methods in ubic.gemma.core.tasks.analysis.diffex that return types with arguments of type ExperimentalFactor

Modifier and Type	Method	Description
Collection<ExperimentalFactor>	DifferentialExpressionAnalysisTaskCommand.getFactors()

Methods in ubic.gemma.core.tasks.analysis.diffex with parameters of type ExperimentalFactor

Modifier and Type	Method	Description
void	DifferentialExpressionAnalysisTaskCommand.setSubsetFactor(ExperimentalFactor subsetFactor)

Method parameters in ubic.gemma.core.tasks.analysis.diffex with type arguments of type ExperimentalFactor

Modifier and Type	Method	Description
void	DifferentialExpressionAnalysisTaskCommand.setFactors(Collection<ExperimentalFactor> factors)

Uses of ExperimentalFactor in ubic.gemma.core.visualization

Methods in ubic.gemma.core.visualization that return types with arguments of type ExperimentalFactor

Modifier and Type	Method	Description
Map<Long,LinkedHashMap<BioAssayValueObject,LinkedHashMap<ExperimentalFactor,Double>>>	ExperimentalDesignVisualizationService.sortVectorDataByDesign(Collection<DoubleVectorValueObject> dedVs, ExperimentalFactor primaryFactor)	Put data vectors in the order you'd want to display the experimental design.
Map<Long,LinkedHashMap<BioAssayValueObject,LinkedHashMap<ExperimentalFactor,Double>>>	ExperimentalDesignVisualizationServiceImpl.sortVectorDataByDesign(Collection<DoubleVectorValueObject> dedVs, ExperimentalFactor primaryFactor)

Methods in ubic.gemma.core.visualization with parameters of type ExperimentalFactor

Modifier and Type	Method	Description
Map<Long,LinkedHashMap<BioAssayValueObject,LinkedHashMap<ExperimentalFactor,Double>>>	ExperimentalDesignVisualizationService.sortVectorDataByDesign(Collection<DoubleVectorValueObject> dedVs, ExperimentalFactor primaryFactor)	Put data vectors in the order you'd want to display the experimental design.
Map<Long,LinkedHashMap<BioAssayValueObject,LinkedHashMap<ExperimentalFactor,Double>>>	ExperimentalDesignVisualizationServiceImpl.sortVectorDataByDesign(Collection<DoubleVectorValueObject> dedVs, ExperimentalFactor primaryFactor)

Uses of ExperimentalFactor in ubic.gemma.core.visualization.cellbrowser

Method parameters in ubic.gemma.core.visualization.cellbrowser with type arguments of type ExperimentalFactor

Modifier and Type	Method	Description
void	CellBrowserMetadataWriter.writeCell(BioAssay bioAssay, String cellId, int cellIndex, List<ExperimentalFactor> factors, Map<ExperimentalFactor,Map<BioMaterial,FactorValue>> factorValueMap, SortedMap<Category,Map<BioAssay,Characteristic>> bioAssayCharacteristics, SortedMap<Category,Map<BioMaterial,Characteristic>> sampleCharacteristics, List<CellLevelCharacteristics> clcs, Writer writer)
void	CellBrowserMetadataWriter.writeCell(BioAssay bioAssay, String cellId, int cellIndex, List<ExperimentalFactor> factors, Map<ExperimentalFactor,Map<BioMaterial,FactorValue>> factorValueMap, SortedMap<Category,Map<BioAssay,Characteristic>> bioAssayCharacteristics, SortedMap<Category,Map<BioMaterial,Characteristic>> sampleCharacteristics, List<CellLevelCharacteristics> clcs, Writer writer)

Uses of ExperimentalFactor in ubic.gemma.model.analysis.expression

Methods in ubic.gemma.model.analysis.expression that return types with arguments of type ExperimentalFactor

Modifier and Type	Method	Description
Set<ExperimentalFactor>	FactorAssociatedAnalysisResultSet.getExperimentalFactors()

Method parameters in ubic.gemma.model.analysis.expression with type arguments of type ExperimentalFactor

Modifier and Type	Method	Description
void	FactorAssociatedAnalysisResultSet.setExperimentalFactors(Set<ExperimentalFactor> experimentalFactors)

Uses of ExperimentalFactor in ubic.gemma.model.analysis.expression.diff

Methods in ubic.gemma.model.analysis.expression.diff that return ExperimentalFactor

Modifier and Type	Method	Description
ExperimentalFactor	Contrast.getExperimentalFactor()

Methods in ubic.gemma.model.analysis.expression.diff with parameters of type ExperimentalFactor

Modifier and Type	Method	Description
static Contrast	Contrast.continuous(ExperimentalFactor ef)	Create a contrast for a continuous factor.

Method parameters in ubic.gemma.model.analysis.expression.diff with type arguments of type ExperimentalFactor

Modifier and Type	Method	Description
static ExpressionAnalysisResultSet	ExpressionAnalysisResultSet.Factory.newInstance(Set<ExperimentalFactor> experimentalFactors, Integer numberOfProbesTested, Integer numberOfGenesTested, FactorValue baselineGroup, Set<DifferentialExpressionAnalysisResult> results, DifferentialExpressionAnalysis analysis, PvalueDistribution pvalueDistribution, Set<HitListSize> hitListSizes)

Uses of ExperimentalFactor in ubic.gemma.model.expression.experiment

Fields in ubic.gemma.model.expression.experiment with type parameters of type ExperimentalFactor

Modifier and Type	Field	Description
static Comparator<ExperimentalFactor>	ExperimentalFactor.COMPARATOR

Methods in ubic.gemma.model.expression.experiment that return ExperimentalFactor

Modifier and Type	Method	Description
ExperimentalFactor	FactorValue.getExperimentalFactor()
static ExperimentalFactor	ExperimentalFactor.Factory.newInstance()
static ExperimentalFactor	ExperimentalFactor.Factory.newInstance(String name, FactorType factorType)
static ExperimentalFactor	ExperimentalFactor.Factory.newInstance(String name, FactorType factorType, Category category)
static ExperimentalFactor	ExperimentalFactor.Factory.newInstance(ExperimentalDesign ed, String name, FactorType factorType)

Methods in ubic.gemma.model.expression.experiment that return types with arguments of type ExperimentalFactor

Modifier and Type	Method	Description
Set<ExperimentalFactor>	ExperimentalDesign.getExperimentalFactors()
static Map<ExperimentalFactor,Map<BioMaterial,FactorValue>>	ExperimentalDesignUtils.getFactorValueMap(Collection<ExperimentalFactor> factors, Collection<BioMaterial> samples)
static Map<ExperimentalFactor,Map<BioMaterial,FactorValue>>	ExperimentalDesignUtils.getFactorValueMap(ExperimentalDesign experimentalDesign, Collection<BioMaterial> samples)	Create a mapping of samples to factor values for all factors in the experimental design.

Methods in ubic.gemma.model.expression.experiment with parameters of type ExperimentalFactor

Modifier and Type	Method	Description
static boolean	ExperimentFactorUtils.isBatchFactor(ExperimentalFactor ef)	Check if a factor is a batch factor.
static FactorValue	FactorValue.Factory.newInstance(ExperimentalFactor experimentalFactor)
static FactorValue	FactorValue.Factory.newInstance(ExperimentalFactor factor, Characteristic c)	Create a FactorValue with a single characteristic.
static FactorValue	FactorValue.Factory.newInstance(ExperimentalFactor factor, Measurement measurement)	Create a FactorValue with a measurement.
static FactorValue	FactorValue.Factory.newInstance(ExperimentalFactor factor, Statement c)	Create a FactorValue with a single statement.
void	FactorValue.setExperimentalFactor(ExperimentalFactor experimentalFactor)

Method parameters in ubic.gemma.model.expression.experiment with type arguments of type ExperimentalFactor

Modifier and Type	Method	Description
static Map<ExperimentalFactor,Map<BioMaterial,FactorValue>>	ExperimentalDesignUtils.getFactorValueMap(Collection<ExperimentalFactor> factors, Collection<BioMaterial> samples)
void	ExperimentalDesign.setExperimentalFactors(Set<ExperimentalFactor> experimentalFactors)

Constructors in ubic.gemma.model.expression.experiment with parameters of type ExperimentalFactor

Modifier	Constructor	Description
	ExperimentalFactorValueObject(ExperimentalFactor factor)
	ExperimentalFactorValueObject(ExperimentalFactor factor, boolean includeValues)

Uses of ExperimentalFactor in ubic.gemma.persistence.service.analysis.expression.diff

Methods in ubic.gemma.persistence.service.analysis.expression.diff with parameters of type ExperimentalFactor

Modifier and Type	Method	Description
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisDao.findByFactor(ExperimentalFactor ef)	Retrieve analyses associated with the factor, either through the subset factor or as factors for result sets.
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisService.findByFactor(ExperimentalFactor ef)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisServiceImpl.findByFactor(ExperimentalFactor ef)
int	DifferentialExpressionAnalysisService.removeForExperimentalFactor(ExperimentalFactor experimentalFactor)	Remove analyses using the given factor.
int	DifferentialExpressionAnalysisServiceImpl.removeForExperimentalFactor(ExperimentalFactor experimentalFactor)

Method parameters in ubic.gemma.persistence.service.analysis.expression.diff with type arguments of type ExperimentalFactor

Modifier and Type	Method	Description
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisDao.findByFactors(Collection<ExperimentalFactor> experimentalFactors)
int	DifferentialExpressionAnalysisService.removeForExperimentalFactors(Collection<ExperimentalFactor> experimentalFactors)
int	DifferentialExpressionAnalysisServiceImpl.removeForExperimentalFactors(Collection<ExperimentalFactor> experimentalFactors)

Uses of ExperimentalFactor in ubic.gemma.persistence.service.expression.biomaterial

Methods in ubic.gemma.persistence.service.expression.biomaterial with parameters of type ExperimentalFactor

Modifier and Type	Method	Description
Collection<BioMaterial>	BioMaterialDao.findByFactor(ExperimentalFactor experimentalFactor)
Collection<BioMaterial>	BioMaterialDaoImpl.findByFactor(ExperimentalFactor experimentalFactor)
Collection<BioMaterial>	BioMaterialService.findByFactor(ExperimentalFactor experimentalFactor)
Collection<BioMaterial>	BioMaterialServiceImpl.findByFactor(ExperimentalFactor experimentalFactor)

Uses of ExperimentalFactor in ubic.gemma.persistence.service.expression.experiment

Methods in ubic.gemma.persistence.service.expression.experiment that return ExperimentalFactor

Modifier and Type	Method	Description
ExperimentalFactor	ExpressionExperimentService.addFactor(ExpressionExperiment ee, ExperimentalFactor factor)
ExperimentalFactor	ExpressionExperimentServiceImpl.addFactor(ExpressionExperiment ee, ExperimentalFactor factor)
ExperimentalFactor	ExperimentalFactorDao.find(ExperimentalFactor experimentalFactor)
ExperimentalFactor	ExperimentalFactorDaoImpl.find(ExperimentalFactor experimentalFactor)
ExperimentalFactor	ExperimentalFactorService.find(ExperimentalFactor experimentalFactor)
ExperimentalFactor	ExperimentalFactorDao.findOrCreate(ExperimentalFactor experimentalFactor)
ExperimentalFactor	ExperimentalFactorService.findOrCreate(ExperimentalFactor experimentalFactor)
ExperimentalFactor	ExperimentalFactorService.load(Long id)
ExperimentalFactor	SingleCellExpressionExperimentService.recreateCellTypeFactor(ExpressionExperiment ee)	Recreate the cell type factor based on the preferred labelling of the preferred single-cell vectors.
ExperimentalFactor	SingleCellExpressionExperimentServiceImpl.recreateCellTypeFactor(ExpressionExperiment ee)
ExperimentalFactor	ExperimentalFactorDao.thaw(ExperimentalFactor ef)
ExperimentalFactor	ExperimentalFactorDaoImpl.thaw(ExperimentalFactor ef)
ExperimentalFactor	ExperimentalFactorService.thaw(ExperimentalFactor ef)
ExperimentalFactor	ExperimentalFactorServiceImpl.thaw(ExperimentalFactor ef)

Methods in ubic.gemma.persistence.service.expression.experiment that return types with arguments of type ExperimentalFactor

Modifier and Type	Method	Description
Optional<ExperimentalFactor>	SingleCellExpressionExperimentService.getCellTypeFactor(ExpressionExperiment ee)	Obtain the cell type factor.
Optional<ExperimentalFactor>	SingleCellExpressionExperimentServiceImpl.getCellTypeFactor(ExpressionExperiment ee)
Map<ExperimentalFactor,Map<FactorValue,ExpressionExperimentSubSet>>	ExpressionExperimentService.getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)	Reconstitute the FV to subset mapping for a given experiment.
Map<ExperimentalFactor,Map<FactorValue,ExpressionExperimentSubSet>>	ExpressionExperimentServiceImpl.getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)
Collection<ExperimentalFactor>	ExperimentalFactorService.load(Collection<Long> ids)
Collection<ExperimentalFactor>	ExperimentalFactorService.loadAll()

Methods in ubic.gemma.persistence.service.expression.experiment with parameters of type ExperimentalFactor

Modifier and Type	Method	Description
ExperimentalFactor	ExpressionExperimentService.addFactor(ExpressionExperiment ee, ExperimentalFactor factor)
ExperimentalFactor	ExpressionExperimentServiceImpl.addFactor(ExpressionExperiment ee, ExperimentalFactor factor)
protected ExperimentalFactorValueObject	ExperimentalFactorDaoImpl.doLoadValueObject(ExperimentalFactor e)
ExperimentalFactor	ExperimentalFactorDao.find(ExperimentalFactor experimentalFactor)
ExperimentalFactor	ExperimentalFactorDaoImpl.find(ExperimentalFactor experimentalFactor)
ExperimentalFactor	ExperimentalFactorService.find(ExperimentalFactor experimentalFactor)
ExpressionExperiment	ExpressionExperimentDao.findByFactor(ExperimentalFactor ef)
ExpressionExperiment	ExpressionExperimentDaoImpl.findByFactor(ExperimentalFactor ef)
ExpressionExperiment	ExpressionExperimentService.findByFactor(ExperimentalFactor factor)
ExpressionExperiment	ExpressionExperimentServiceImpl.findByFactor(ExperimentalFactor factor)
ExperimentalFactor	ExperimentalFactorDao.findOrCreate(ExperimentalFactor experimentalFactor)
ExperimentalFactor	ExperimentalFactorService.findOrCreate(ExperimentalFactor experimentalFactor)
Collection<FactorValue>	ExpressionExperimentSubSetDao.getFactorValuesUsed(ExpressionExperimentSubSet entity, ExperimentalFactor factor)	Obtain the FactorValue used by the samples from this subset in the given factor.
Collection<FactorValue>	ExpressionExperimentSubSetDaoImpl.getFactorValuesUsed(ExpressionExperimentSubSet entity, ExperimentalFactor factor)
Collection<FactorValue>	ExpressionExperimentSubSetService.getFactorValuesUsed(ExpressionExperimentSubSet entity, ExperimentalFactor factor)
Collection<FactorValue>	ExpressionExperimentSubSetServiceImpl.getFactorValuesUsed(ExpressionExperimentSubSet entity, ExperimentalFactor factor)
Map<FactorValue,ExpressionExperimentSubSet>	ExpressionExperimentService.getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension)	Reconstitute the FV to subset mapping for a given experiment and factor.
Map<FactorValue,ExpressionExperimentSubSet>	ExpressionExperimentServiceImpl.getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension)
Map<FactorValue,ExpressionExperimentSubSet>	ExpressionExperimentService.getSubSetsByFactorValueWithCharacteristicsAndBioAssays(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension)	Reconstitute the FV to subset mapping for a given experiment and factor.
Map<FactorValue,ExpressionExperimentSubSet>	ExpressionExperimentServiceImpl.getSubSetsByFactorValueWithCharacteristicsAndBioAssays(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension)
void	ExperimentalFactorDaoImpl.remove(ExperimentalFactor experimentalFactor)
void	ExperimentalFactorService.remove(ExperimentalFactor experimentalFactor)	Delete the factor, its associated factor values and all differential expression analyses in which it is used.
void	ExperimentalFactorServiceImpl.remove(ExperimentalFactor experimentalFactor)
ExperimentalFactor	ExperimentalFactorDao.thaw(ExperimentalFactor ef)
ExperimentalFactor	ExperimentalFactorDaoImpl.thaw(ExperimentalFactor ef)
ExperimentalFactor	ExperimentalFactorService.thaw(ExperimentalFactor ef)
ExperimentalFactor	ExperimentalFactorServiceImpl.thaw(ExperimentalFactor ef)
void	ExperimentalFactorService.update(ExperimentalFactor experimentalFactor)

Method parameters in ubic.gemma.persistence.service.expression.experiment with type arguments of type ExperimentalFactor

Modifier and Type	Method	Description
Collection<ExpressionExperiment>	ExpressionExperimentDao.findByFactors(Collection<ExperimentalFactor> factors)
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.findByFactors(Collection<ExperimentalFactor> factors)
Collection<ExpressionExperiment>	ExpressionExperimentService.findByFactors(Collection<ExperimentalFactor> factors)
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.findByFactors(Collection<ExperimentalFactor> factors)
void	ExperimentalFactorService.remove(Collection<ExperimentalFactor> entities)
void	ExperimentalFactorServiceImpl.remove(Collection<ExperimentalFactor> experimentalFactors)
void	ExperimentalFactorService.update(Collection<ExperimentalFactor> entities)

Uses of ExperimentalFactor in ubic.gemma.persistence.util

Methods in ubic.gemma.persistence.util that return types with arguments of type ExperimentalFactor

Modifier and Type	Method	Description
List<ExperimentalFactor>	FactorValueVector.getFactors()

Methods in ubic.gemma.persistence.util with parameters of type ExperimentalFactor

Modifier and Type	Method	Description
static void	BusinessKey.addRestrictions(Criteria queryObject, ExperimentalFactor experimentalFactor)
static void	BusinessKey.checkValidKey(ExperimentalFactor experimentalFactor)
Collection<FactorValue>	FactorValueVector.getValuesForFactor(ExperimentalFactor factor)

Constructor parameters in ubic.gemma.persistence.util with type arguments of type ExperimentalFactor

Modifier	Constructor	Description
	FactorValueVector(Collection<ExperimentalFactor> factors, Collection<FactorValue> values)

Uses of ExperimentalFactor in ubic.gemma.web.controller.expression.experiment

Method parameters in ubic.gemma.web.controller.expression.experiment with type arguments of type ExperimentalFactor

Modifier and Type	Method	Description
void	ExperimentalDesignController.createFactorValue(EntityDelegator<ExperimentalFactor> e)	AJAX
void	ExperimentalDesignController.deleteFactorValues(EntityDelegator<ExperimentalFactor> e, Long[] fvIds)	AJAX
void	ExperimentalDesignController.duplicateFactorValue(EntityDelegator<ExperimentalFactor> e, Long fvId)	Make an exact copy of a factorvalue and add it to the experiment.
Collection<FactorValueValueObject>	ExperimentalDesignController.getFactorValues(EntityDelegator<ExperimentalFactor> e)	AJAX
Collection<FactorValueValueObject>	ExpressionExperimentController.getFactorValues(EntityDelegator<ExperimentalFactor> e)	AJAX
Collection<FactorValueValueObject>	ExperimentalDesignController.getFactorValuesWithCharacteristics(EntityDelegator<ExperimentalFactor> e)	AJAX

Uses of ExperimentalFactor in ubic.gemma.web.controller.visualization

Method parameters in ubic.gemma.web.controller.visualization with type arguments of type ExperimentalFactor

Modifier and Type	Method	Description
void	VisualizationValueObject.setUpFactorProfiles(LinkedHashMap<BioAssayValueObject,LinkedHashMap<ExperimentalFactor,Double>> layout)	Initialize the factor profiles.

Constructors in ubic.gemma.web.controller.visualization with parameters of type ExperimentalFactor

Modifier	Constructor	Description
	FactorProfile(ExperimentalFactor ef, LinkedHashMap<BioAssayValueObject,LinkedHashMap<ExperimentalFactor,Double>> layouts)

Constructor parameters in ubic.gemma.web.controller.visualization with type arguments of type ExperimentalFactor

Modifier	Constructor	Description
	FactorProfile(ExperimentalFactor ef, LinkedHashMap<BioAssayValueObject,LinkedHashMap<ExperimentalFactor,Double>> layouts)