Uses of Class
ubic.gemma.model.expression.bioAssayData.DataVector

Packages that use DataVector

Package	Description
ubic.gemma.apps	This package contains built-in Gemma CLI applications.
ubic.gemma.cli.util
ubic.gemma.core.analysis.preprocess.convert	Convert data from one QuantitationType to another.
ubic.gemma.core.analysis.stats	This package contains classes for computing various statistics.
ubic.gemma.core.datastructure.matrix.io	This package contains I/O utilities for reading and writing expression data matrices.
ubic.gemma.model.common.quantitationtype
ubic.gemma.model.expression.bioAssayData
ubic.gemma.persistence.service.common.quantitationtype
ubic.gemma.persistence.service.expression.experiment

Uses of DataVector in ubic.gemma.apps

Classes in ubic.gemma.apps with type parameters of type DataVector

Modifier and Type	Class	Description
class	ExpressionExperimentVectorsManipulatingCli<T extends DataVector>	Base class for CLI tools that manipulate expression experiment vectors.

Method parameters in ubic.gemma.apps with type arguments of type DataVector

Modifier and Type	Method	Description
protected void	DetectQuantitationTypeCli.processExpressionExperimentVectors(ExpressionExperiment ee, QuantitationType qt, Class<? extends DataVector> vectorType)

Uses of DataVector in ubic.gemma.cli.util

Methods in ubic.gemma.cli.util with type parameters of type DataVector

Modifier and Type	Method	Description
<T extends DataVector> QuantitationType	EntityLocator.locateQuantitationType(ExpressionExperiment ee, String qt, Class<? extends T> vectorType)
<T extends DataVector> Map.Entry<Class<? extends T>,QuantitationType>	EntityLocator.locateQuantitationType(ExpressionExperiment ee, String qt, Collection<Class<? extends T>> vectorType)
<T extends DataVector> QuantitationType	EntityLocatorImpl.locateQuantitationType(ExpressionExperiment ee, String qt, Class<? extends T> vectorType)
<T extends DataVector> org.apache.commons.lang3.tuple.Pair<Class<? extends T>,QuantitationType>	EntityLocatorImpl.locateQuantitationType(ExpressionExperiment ee, String qt, Collection<Class<? extends T>> vectorTypes)

Uses of DataVector in ubic.gemma.core.analysis.preprocess.convert

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

Modifier and Type	Method	Description
static <T extends DataVector> Collection<T>	RepresentationConversionUtils.convertVectors(Collection<T> vectors, PrimitiveType toRepresentation, Class<T> vectorType)	Convert a collection of vectors to a desired representation.
static <T extends DataVector> Collection<T>	ScaleTypeConversionUtils.convertVectors(Collection<T> vectors, ScaleType toScale, Class<T> vectorType)

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

Modifier and Type	Method	Description
static double[]	ScaleTypeConversionUtils.convertData(DataVector vec, ScaleType scaleType)	Convert a vector to the target scale.

Uses of DataVector in ubic.gemma.core.analysis.stats

Methods in ubic.gemma.core.analysis.stats with parameters of type DataVector

Modifier and Type	Method	Description
static int	DataVectorDescriptive.count(DataVector vector)	Count the number of values in a vector.
static int	DataVectorDescriptive.countMissing(DataVector vector)	Count the number of missing values.
static double	DataVectorDescriptive.mean(DataVector vector)	Calculate the mean of the data in the vector.
static double	DataVectorDescriptive.sampleStandardDeviation(DataVector vector)
static double	DataVectorDescriptive.sampleVariance(DataVector vector)
static double	DataVectorDescriptive.sum(DataVector vector)

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

Classes in ubic.gemma.core.datastructure.matrix.io with type parameters of type DataVector

Modifier and Type	Interface	Description
interface	ExpressionDataMatrixWriter<T extends ExpressionDataMatrix<?>,VT extends DataVector>	Base interface for writing ExpressionDataMatrix.

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

Modifier and Type	Method	Description
static void	ExpressionDataWriterUtils.appendBaseHeader(ExpressionExperiment experiment, QuantitationType quantitationType, Class<? extends DataVector> dataVectorType, String fileTypeStr, String experimentUrl, BuildInfo buildInfo, Date timestamp, Writer buf)	Append base header information (about the experiment) to a file with some information about the quantitation type.
static String	ExpressionDataWriterUtils.formatQuantitationType(QuantitationType quantitationType, Class<? extends DataVector> dataVectorType)

Uses of DataVector in ubic.gemma.model.common.quantitationtype

Constructor parameters in ubic.gemma.model.common.quantitationtype with type arguments of type DataVector

Modifier	Constructor	Description
	QuantitationTypeValueObject(QuantitationType qt, ExpressionExperiment expressionExperiment, Class<? extends DataVector> vectorType)	Create a QuantitationType VO in the context of an associated experiment.

Uses of DataVector in ubic.gemma.model.expression.bioAssayData

Subclasses of DataVector in ubic.gemma.model.expression.bioAssayData

Modifier and Type	Class	Description
class	BulkExpressionDataVector	A data vector storing bulk expression data.
class	DesignElementDataVector	Data vector associated to a CompositeSequence.
class	ProcessedExpressionDataVector	Represents the processed data that is used for actual analyses.
class	RawExpressionDataVector	Data for one design element, across one or more bioassays, for a single quantitation type.
class	SingleCellExpressionDataVector	An expression data vector that contains data at the resolution of individual cells.

Uses of DataVector in ubic.gemma.persistence.service.common.quantitationtype

Methods in ubic.gemma.persistence.service.common.quantitationtype with type parameters of type DataVector

Modifier and Type	Method	Description
<T extends DataVector> Collection<QuantitationType>	QuantitationTypeDao.findAllByNameAndVectorType(ExpressionExperiment ee, String name, Class<? extends T> vectorType)
<T extends DataVector> Collection<QuantitationType>	QuantitationTypeDaoImpl.findAllByNameAndVectorType(ExpressionExperiment ee, String name, Class<? extends T> vectorType)
<T extends DataVector> Collection<QuantitationType>	QuantitationTypeService.findAllByNameAndVectorType(ExpressionExperiment ee, String name, Class<? extends T> vectorType)	Find all the QT associated to the given experiment, name and vector type.
<T extends DataVector> Collection<QuantitationType>	QuantitationTypeServiceImpl.findAllByNameAndVectorType(ExpressionExperiment ee, String name, Class<? extends T> vectorType)
<T extends DataVector> Collection<QuantitationType>	QuantitationTypeService.findByExpressionExperiment(ExpressionExperiment ee, Class<? extends T> dataVectorType)	Find all the QT associated to the given experiment and data vector type.
<T extends DataVector> Collection<QuantitationType>	QuantitationTypeService.findByExpressionExperiment(ExpressionExperiment ee, Collection<Class<? extends T>> vectorTypes)
<T extends DataVector> Collection<QuantitationType>	QuantitationTypeServiceImpl.findByExpressionExperiment(ExpressionExperiment ee, Class<? extends T> dataVectorType)
<T extends DataVector> Collection<QuantitationType>	QuantitationTypeServiceImpl.findByExpressionExperiment(ExpressionExperiment ee, Collection<Class<? extends T>> vectorTypes)
<T extends DataVector> Collection<Class<? extends T>>	QuantitationTypeService.getMappedDataVectorType(Class<T> vectorType)	Infer all the mapped vector types that are subclasses of the given vector type.
<T extends DataVector> Collection<Class<? extends T>>	QuantitationTypeServiceImpl.getMappedDataVectorType(Class<T> vectorType)
<T extends DataVector> Collection<Class<? extends T>>	QuantitationTypeDao.getMappedDataVectorTypes(Class<T> vectorType)	Obtain the vector types that are mapped and subclass of the given vector type.
<T extends DataVector> Collection<Class<? extends T>>	QuantitationTypeDaoImpl.getMappedDataVectorTypes(Class<T> vectorType)

Methods in ubic.gemma.persistence.service.common.quantitationtype that return types with arguments of type DataVector

Modifier and Type	Method	Description
Map<Class<? extends DataVector>,Set<QuantitationType>>	QuantitationTypeDao.findByExpressionExperiment(ExpressionExperiment ee)	Retrieve all the QTs associated with the given experiment.
Map<Class<? extends DataVector>,Set<QuantitationType>>	QuantitationTypeDaoImpl.findByExpressionExperiment(ExpressionExperiment ee)
Map<Class<? extends DataVector>,Set<QuantitationType>>	QuantitationTypeService.findByExpressionExperiment(ExpressionExperiment ee)	Find all the QT associated to the given experiment.
Map<Class<? extends DataVector>,Set<QuantitationType>>	QuantitationTypeServiceImpl.findByExpressionExperiment(ExpressionExperiment ee)
Class<? extends DataVector>	QuantitationTypeDao.getDataVectorType(QuantitationType qt)
Class<? extends DataVector>	QuantitationTypeDaoImpl.getDataVectorType(QuantitationType qt)
Class<? extends DataVector>	QuantitationTypeService.getDataVectorType(QuantitationType qt)
Class<? extends DataVector>	QuantitationTypeServiceImpl.getDataVectorType(QuantitationType qt)
Map<QuantitationType,Class<? extends DataVector>>	QuantitationTypeService.getDataVectorTypes(Collection<QuantitationType> qts)
Map<QuantitationType,Class<? extends DataVector>>	QuantitationTypeServiceImpl.getDataVectorTypes(Collection<QuantitationType> qts)
Collection<Class<? extends DataVector>>	QuantitationTypeDao.getVectorTypes()	Obtain all the data vector types that are associated with quantitation types.
Set<Class<? extends DataVector>>	QuantitationTypeDaoImpl.getVectorTypes()
Collection<Class<? extends DataVector>>	QuantitationTypeService.getVectorTypes()
Collection<Class<? extends DataVector>>	QuantitationTypeServiceImpl.getVectorTypes()

Method parameters in ubic.gemma.persistence.service.common.quantitationtype with type arguments of type DataVector

Modifier and Type	Method	Description
QuantitationType	QuantitationTypeDao.create(QuantitationType quantitationType, Class<? extends DataVector> dataVectorType)
QuantitationType	QuantitationTypeDaoImpl.create(QuantitationType quantitationType, Class<? extends DataVector> dataVectorType)
QuantitationType	QuantitationTypeService.create(QuantitationType quantitationType, Class<? extends DataVector> dataVectorType)	Create a new QuantitationType for the given vector type.
QuantitationType	QuantitationTypeServiceImpl.create(QuantitationType quantitationType, Class<? extends DataVector> dataVectorType)
QuantitationType	QuantitationTypeDao.find(QuantitationType entity, Class<? extends DataVector> dataVectorType)	Find a QT matching the given template for the given data vector type as per QuantitationTypeDao.find(QuantitationType).
QuantitationType	QuantitationTypeDao.find(ExpressionExperiment ee, QuantitationType quantitationType, Set<Class<? extends DataVector>> dataVectorTypes)	Find a QT matching the given template as per QuantitationTypeDao.find(QuantitationType) in a given experiment for and for a given data vector type.
QuantitationType	QuantitationTypeDaoImpl.find(QuantitationType entity, Class<? extends DataVector> dataVectorType)
QuantitationType	QuantitationTypeDaoImpl.find(ExpressionExperiment ee, QuantitationType quantitationType, Set<Class<? extends DataVector>> dataVectorTypes)
QuantitationType	QuantitationTypeService.find(ExpressionExperiment ee, QuantitationType quantitationType, Class<? extends DataVector> dataVectorTypes)	Locate a QT associated with the given ee matching the specification of the passed quantitationType, or null if there isn't one.
QuantitationType	QuantitationTypeServiceImpl.find(ExpressionExperiment ee, QuantitationType quantitationType, Class<? extends DataVector> dataVectorTypes)
Collection<QuantitationType>	QuantitationTypeDao.findByExpressionExperiment(ExpressionExperiment ee, Class<? extends DataVector> dataVectorType)
Collection<QuantitationType>	QuantitationTypeDaoImpl.findByExpressionExperiment(ExpressionExperiment ee, Class<? extends DataVector> vectorType)
QuantitationType	QuantitationTypeDao.findByNameAndVectorType(ExpressionExperiment ee, String name, Class<? extends DataVector> dataVectorType)	Find a quantitation type by experiment, name and data vector type.
QuantitationType	QuantitationTypeDaoImpl.findByNameAndVectorType(ExpressionExperiment ee, String name, Class<? extends DataVector> dataVectorType)
QuantitationType	QuantitationTypeService.findByNameAndVectorType(ExpressionExperiment ee, String name, Class<? extends DataVector> dataVectorType)
QuantitationType	QuantitationTypeServiceImpl.findByNameAndVectorType(ExpressionExperiment ee, String name, Class<? extends DataVector> dataVectorType)
QuantitationType	QuantitationTypeDao.findOrCreate(QuantitationType quantitationType, Class<? extends DataVector> dataVectorType)	Find a QT as per QuantitationTypeDao.find(QuantitationType, Class) and if none is found, create a new one with QuantitationTypeDao.create(QuantitationType, Class).
QuantitationType	QuantitationTypeDaoImpl.findOrCreate(QuantitationType quantitationType, Class<? extends DataVector> dataVectorType)
QuantitationType	QuantitationTypeService.findOrCreate(QuantitationType quantitationType, Class<? extends DataVector> dataVectorType)
QuantitationType	QuantitationTypeServiceImpl.findOrCreate(QuantitationType quantitationType, Class<? extends DataVector> dataVectorType)
QuantitationType	QuantitationTypeDao.loadByIdAndVectorType(Long id, ExpressionExperiment ee, Class<? extends DataVector> dataVectorType)	Load a QT from an experiment by ID and vector type.
QuantitationType	QuantitationTypeDaoImpl.loadByIdAndVectorType(Long id, ExpressionExperiment ee, Class<? extends DataVector> dataVectorType)
QuantitationType	QuantitationTypeService.loadByIdAndVectorType(Long id, ExpressionExperiment ee, Class<? extends DataVector> dataVectorType)	Find a quantitation type by ID and vector type.
QuantitationType	QuantitationTypeServiceImpl.loadByIdAndVectorType(Long id, ExpressionExperiment ee, Class<? extends DataVector> dataVectorType)

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

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

Modifier and Type	Method	Description
Map<Class<? extends DataVector>,Set<QuantitationType>>	ExpressionExperimentService.getQuantitationTypesByVectorType(ExpressionExperiment ee)
Map<Class<? extends DataVector>,Set<QuantitationType>>	ExpressionExperimentServiceImpl.getQuantitationTypesByVectorType(ExpressionExperiment ee)

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

Modifier and Type	Method	Description
Collection<ArrayDesign>	ExpressionExperimentDao.getArrayDesignsUsed(ExpressionExperiment ee, QuantitationType qt, Class<? extends DataVector> dataVectorType)
Collection<ArrayDesign>	ExpressionExperimentDaoImpl.getArrayDesignsUsed(ExpressionExperiment ee, QuantitationType qt, Class<? extends DataVector> dataVectorType)
Collection<ArrayDesign>	ExpressionExperimentService.getArrayDesignsUsed(ExpressionExperiment ee, QuantitationType qt, Class<? extends DataVector> vectorType)	Obtain a collection of ArrayDesign used by a specific set of vectors.
Collection<ArrayDesign>	ExpressionExperimentServiceImpl.getArrayDesignsUsed(ExpressionExperiment ee, QuantitationType qt, Class<? extends DataVector> vectorType)