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

Packages that use FactorValue

Package	Description
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.datastructure.matrix
ubic.gemma.core.ontology
ubic.gemma.model.analysis.expression.diff
ubic.gemma.model.expression.biomaterial
ubic.gemma.model.expression.experiment
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.util
ubic.gemma.web.controller.expression.biomaterial
ubic.gemma.web.controller.expression.experiment

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

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

Modifier and Type	Method	Description
FactorValue	DifferentialExpressionAnalysisConfig.getSubsetFactorValue()

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

Modifier and Type	Method	Description
Map<ExperimentalFactor,FactorValue>	DifferentialExpressionAnalysisConfig.getBaseLineFactorValues()

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

Modifier and Type	Method	Description
static boolean	BaselineSelection.isBaselineCondition(FactorValue factorValue)	Check if a given factor value indicates a baseline condition.
static boolean	BaselineSelection.isForcedBaseline(FactorValue fv)	Check if this factor value is the baseline, overriding other possible baselines.
void	DifferentialExpressionAnalysisConfig.setSubsetFactorValue(FactorValue subsetFactorValue)

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

Modifier and Type	Method	Description
static void	LinearModelAnalyzer.populateFactorValuesFromBASet(BioAssaySet ee, ExperimentalFactor f, Collection<FactorValue> fvs)
void	DifferentialExpressionAnalysisConfig.setBaseLineFactorValues(Map<ExperimentalFactor,FactorValue> baseLineFactorValues)

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

Methods in ubic.gemma.core.datastructure.matrix that return types with arguments of type FactorValue

Modifier and Type	Method	Description
static Map<ExperimentalFactor,FactorValue>	ExpressionDataMatrixColumnSort.getBaselineLevels(Collection<ExperimentalFactor> factors)	Identify the FactorValue that should be treated as 'Baseline' for each of the given factors.
static Map<ExperimentalFactor,FactorValue>	ExpressionDataMatrixColumnSort.getBaselineLevels(List<BioMaterial> samplesUsed, Collection<ExperimentalFactor> factors)	Identify the FactorValue that should be treated as 'Baseline' for each of the given factors.

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

Modifier and Type	Method	Description
static String	ExpressionDataWriterUtils.constructFactorValueName(FactorValue factorValue)	Produce a value for representing a factor value.

Uses of FactorValue in ubic.gemma.core.ontology

Methods in ubic.gemma.core.ontology with parameters of type FactorValue

Modifier and Type	Method	Description
static Map<String,FactorValueOntologyUtils.Annotation>	FactorValueOntologyUtils.getAnnotationsById(FactorValue fv)	Create a mapping of annotation IDs to annotations for a FactorValue.
static String	FactorValueOntologyUtils.getUri(FactorValue factorValue)	Obtain a suitable ontology ID for a given factor value.

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

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

Modifier and Type	Method	Description
FactorValue	ExpressionAnalysisResultSet.getBaselineGroup()
FactorValue	Baseline.getFactorValue()
FactorValue	Contrast.getFactorValue()
FactorValue	ContrastResult.getFactorValue()
FactorValue	Baseline.getSecondFactorValue()
FactorValue	Contrast.getSecondFactorValue()
FactorValue	ContrastResult.getSecondFactorValue()
FactorValue	DifferentialExpressionAnalysis.getSubsetFactorValue()	If non-null, a factor value applicable to the ExpressionExperimentSubSet being analyzed.

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

Modifier and Type	Method	Description
List<FactorValue>	Contrast.getFactorValues()

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

Modifier and Type	Method	Description
static Baseline	Baseline.categorical(FactorValue fv)	Create a baseline for a single categorical factor.
static Contrast	Contrast.categorical(FactorValue fv)	Create a contrast for a categorical factor.
static Baseline	Baseline.interaction(FactorValue fv1, FactorValue fv2)	Create a baseline for an interaction of factors.
static Contrast	Contrast.interaction(FactorValue fv1, FactorValue fv2)	Create an interaction of two categorical factors.
static ContrastResult	ContrastResult.Factory.newInstance(Double pvalue, Double tstat, Double coefficient, Double logFoldChange, FactorValue factorValue, FactorValue secondFactorValue)
static ExpressionAnalysisResultSet	ExpressionAnalysisResultSet.Factory.newInstance(Set<ExperimentalFactor> experimentalFactors, Integer numberOfProbesTested, Integer numberOfGenesTested, FactorValue baselineGroup, Set<DifferentialExpressionAnalysisResult> results, DifferentialExpressionAnalysis analysis, PvalueDistribution pvalueDistribution, Set<HitListSize> hitListSizes)
void	ExpressionAnalysisResultSet.setBaselineGroup(FactorValue baselineGroup)
void	ContrastResult.setFactorValue(FactorValue factorValue)
void	ContrastResult.setSecondFactorValue(FactorValue secondFactorValue)
void	DifferentialExpressionAnalysis.setSubsetFactorValue(FactorValue subsetFactorValue)

Uses of FactorValue in ubic.gemma.model.expression.biomaterial

Methods in ubic.gemma.model.expression.biomaterial that return types with arguments of type FactorValue

Modifier and Type	Method	Description
Set<FactorValue>	BioMaterial.getFactorValues()

Method parameters in ubic.gemma.model.expression.biomaterial with type arguments of type FactorValue

Modifier and Type	Method	Description
void	BioMaterial.setFactorValues(Set<FactorValue> factorValues)

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

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

Modifier and Type	Method	Description
static FactorValue	FactorValue.Factory.newInstance()
static FactorValue	FactorValue.Factory.newInstance(ExperimentalFactor experimentalFactor)

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

Modifier and Type	Method	Description
static Map<ExperimentalFactor,FactorValue>	ExperimentalDesignUtils.getBaselineConditions(List<BioMaterial> samplesUsed, List<ExperimentalFactor> factors)
Set<FactorValue>	ExperimentalFactor.getFactorValues()

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

Modifier and Type	Method	Description
static String	FactorValueUtils.getSummaryString(FactorValue fv)	Produce a summary string for this factor value.
static String	FactorValueUtils.getSummaryString(FactorValue fv, String statementDelimiter)
static String	ExperimentalDesignUtils.nameForR(FactorValue fv, boolean isBaseline)

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

Modifier and Type	Method	Description
static ObjectMatrix<String,String,Object>	ExperimentalDesignUtils.buildDesignMatrix(List<ExperimentalFactor> factors, List<BioMaterial> samplesUsed, Map<ExperimentalFactor,FactorValue> baselines)	Convert factors to a matrix usable in R.
static boolean	ExperimentalDesignUtils.isComplete(ExperimentalFactor factor, List<BioMaterial> samplesUsed, Map<ExperimentalFactor,FactorValue> baselines)	Check if a factor has missing values (samples that lack an assigned value)
static ObjectMatrix<BioMaterial,ExperimentalFactor,Object>	ExperimentalDesignUtils.sampleInfoMatrix(List<ExperimentalFactor> factors, List<BioMaterial> samplesUsed, Map<ExperimentalFactor,FactorValue> baselines)
void	ExperimentalFactor.setFactorValues(Set<FactorValue> factorValues)

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

Constructor	Description
AbstractFactorValueValueObject(FactorValue fv, boolean includeExperimentalFactor)
FactorValueBasicValueObject(FactorValue fv)
FactorValueValueObject(FactorValue value)	Deprecated.
FactorValueValueObject(FactorValue value, boolean includeExperimentalFactor)	Deprecated. Create a FactorValue VO.
FactorValueValueObject(FactorValue fv, Statement c)	Deprecated. Create a FactorValue VO focusing on a specific statement.

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

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

Modifier and Type	Method	Description
FactorValue	ExpressionExperimentService.addFactorValue(ExpressionExperiment ee, FactorValue fv)
FactorValue	ExpressionExperimentServiceImpl.addFactorValue(ExpressionExperiment ee, FactorValue fv)
FactorValue	FactorValueDaoImpl.create(FactorValue factorValue)
FactorValue	FactorValueDaoImpl.find(FactorValue factorValue)
FactorValue	FactorValueService.findOrCreate(FactorValue factorValue)
FactorValue	FactorValueService.load(Long id)
FactorValue	FactorValueService.loadWithExperimentalFactor(Long id)
FactorValue	FactorValueServiceImpl.loadWithExperimentalFactor(Long id)
FactorValue	FactorValueService.loadWithExperimentalFactorOrFail(Long id)	Load a FactorValue with an initialized experimental factor or fail.
FactorValue	FactorValueServiceImpl.loadWithExperimentalFactorOrFail(Long id)
FactorValue	FactorValueDao.loadWithOldStyleCharacteristics(Long id, boolean readOnly)	Deprecated.
FactorValue	FactorValueDaoImpl.loadWithOldStyleCharacteristics(Long id, boolean readOnly)	Deprecated.
FactorValue	FactorValueService.loadWithOldStyleCharacteristics(Long id, boolean readOnly)	Deprecated. do not use this, it is only meant for the purpose of migrating old-style characteristics to statements
FactorValue	FactorValueServiceImpl.loadWithOldStyleCharacteristics(Long id, boolean readOnly)	Deprecated.
FactorValue	FactorValueDaoImpl.save(FactorValue entity)

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

Modifier and Type	Method	Description
Map<ExpressionExperiment,FactorValue>	ExpressionExperimentDao.findByFactorValues(Collection<FactorValue> fvs)
Map<ExpressionExperiment,FactorValue>	ExpressionExperimentDaoImpl.findByFactorValues(Collection<FactorValue> fvs)
Map<ExpressionExperiment,FactorValue>	ExpressionExperimentService.findByFactorValues(Collection<FactorValue> factorValues)
Map<ExpressionExperiment,FactorValue>	ExpressionExperimentServiceImpl.findByFactorValues(Collection<FactorValue> factorValues)
Collection<FactorValue>	FactorValueDao.findByValue(String valuePrefix)	Deprecated.
Collection<FactorValue>	FactorValueDaoImpl.findByValue(String valuePrefix)
Collection<FactorValue>	FactorValueService.findByValue(String valuePrefix)	Deprecated.
Collection<FactorValue>	FactorValueServiceImpl.findByValue(String valuePrefix)	Deprecated.
Collection<FactorValue>	ExpressionExperimentSubSetDao.getFactorValuesUsed(ExpressionExperimentSubSet entity, ExperimentalFactor 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)

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

Modifier and Type	Method	Description
FactorValue	ExpressionExperimentService.addFactorValue(ExpressionExperiment ee, FactorValue fv)
FactorValue	ExpressionExperimentServiceImpl.addFactorValue(ExpressionExperiment ee, FactorValue fv)
void	FactorValueService.clearNeedsAttentionFlag(FactorValue factorValue, String note)	Clear a needs attention flag on a given factor value.
void	FactorValueServiceImpl.clearNeedsAttentionFlag(FactorValue factorValue, String note)
FactorValue	FactorValueDaoImpl.create(FactorValue factorValue)
Statement	FactorValueService.createStatement(FactorValue factorValue, Statement statement)	Create a given statement and add it to the given factor value.
Statement	FactorValueServiceImpl.createStatement(FactorValue factorValue, Statement statement)
protected FactorValueValueObject	FactorValueDaoImpl.doLoadValueObject(FactorValue entity)
FactorValue	FactorValueDaoImpl.find(FactorValue factorValue)
ExpressionExperiment	ExpressionExperimentDao.findByFactorValue(FactorValue fv)
ExpressionExperiment	ExpressionExperimentDaoImpl.findByFactorValue(FactorValue fv)
ExpressionExperiment	ExpressionExperimentService.findByFactorValue(FactorValue factorValue)
ExpressionExperiment	ExpressionExperimentServiceImpl.findByFactorValue(FactorValue factorValue)
FactorValue	FactorValueService.findOrCreate(FactorValue factorValue)
void	FactorValueService.markAsNeedsAttention(FactorValue factorValue, String note)	Mark a given factor value as needs attention.
void	FactorValueServiceImpl.markAsNeedsAttention(FactorValue factorValue, String note)
void	FactorValueDaoImpl.remove(FactorValue factorValue)
void	FactorValueService.remove(FactorValue factorValue)
void	FactorValueServiceImpl.remove(FactorValue entity)
void	FactorValueService.removeStatement(FactorValue fv, Statement c)	Remove a statement from a factor value.
void	FactorValueServiceImpl.removeStatement(FactorValue fv, Statement statement)
FactorValue	FactorValueDaoImpl.save(FactorValue entity)
Statement	FactorValueService.saveStatement(FactorValue fv, Statement statement)	Create a given statement as per FactorValueService.createStatement(FactorValue, Statement) if it is transient, otherwise update an existing statement.
Statement	FactorValueServiceImpl.saveStatement(FactorValue fv, Statement statement)
Statement	FactorValueService.saveStatementIgnoreAcl(FactorValue fv, Statement statement)	Deprecated. do not use this, it is meant for FactorValue migration only
Statement	FactorValueServiceImpl.saveStatementIgnoreAcl(FactorValue fv, Statement statement)
void	FactorValueDaoImpl.update(FactorValue entity)
void	FactorValueService.update(FactorValue factorValue)
void	FactorValueDao.updateIgnoreAcl(FactorValue fv)	Deprecated. do not use this, it is only a workaround to make FV migration faster
void	FactorValueDaoImpl.updateIgnoreAcl(FactorValue fv)

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

Modifier and Type	Method	Description
void	ExpressionExperimentService.addFactorValues(ExpressionExperiment ee, Map<BioMaterial,FactorValue> fvs)	Intended with the case of a continuous factor being added.
void	ExpressionExperimentServiceImpl.addFactorValues(ExpressionExperiment ee, Map<BioMaterial,FactorValue> fvs)
Map<ExpressionExperiment,FactorValue>	ExpressionExperimentDao.findByFactorValues(Collection<FactorValue> fvs)
Map<ExpressionExperiment,FactorValue>	ExpressionExperimentDaoImpl.findByFactorValues(Collection<FactorValue> fvs)
Map<ExpressionExperiment,FactorValue>	ExpressionExperimentService.findByFactorValues(Collection<FactorValue> factorValues)
Map<ExpressionExperiment,FactorValue>	ExpressionExperimentServiceImpl.findByFactorValues(Collection<FactorValue> factorValues)
void	FactorValueServiceImpl.remove(Collection<FactorValue> entities)
void	FactorValueService.update(Collection<FactorValue> factorValues)

Uses of FactorValue in ubic.gemma.persistence.util

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

Modifier and Type	Method	Description
Collection<FactorValue>	FactorValueVector.getValuesForFactor(ExperimentalFactor factor)

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

Modifier and Type	Method	Description
static void	BusinessKey.checkKey(FactorValue factorValue)
int	FactorValueComparator.compare(FactorValue v1, FactorValue v2)
static void	BusinessKey.createQueryObject(Criteria queryObject, FactorValue factorValue)

Uses of FactorValue in ubic.gemma.web.controller.expression.biomaterial

Method parameters in ubic.gemma.web.controller.expression.biomaterial with type arguments of type FactorValue

Modifier and Type	Method	Description
void	BioMaterialController.addFactorValueTo(Collection<Long> bmIds, EntityDelegator<FactorValue> factorValueId)	AJAX

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

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

Modifier and Type	Method	Description
void	ExperimentalDesignController.createFactorValueCharacteristic(EntityDelegator<FactorValue> e, CharacteristicValueObject cvo)