Uses of Interface
ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix

Packages that use ExpressionDataMatrix

Package	Description
ubic.gemma.core.analysis.preprocess.detect	This package contains classes for detecting and linting expression data.
ubic.gemma.core.analysis.preprocess.filter	This package contains classes for filtering expression 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.

Uses of ExpressionDataMatrix in ubic.gemma.core.analysis.preprocess.detect

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

Modifier and Type	Method	Description
static QuantitationType	QuantitationTypeDetectionUtils.inferQuantitationType(ExpressionDataMatrix<?> expressionDataDoubleMatrix)	Infer a QuantitationType from expression data.
static void	QuantitationTypeDetectionUtils.lintQuantitationType(QuantitationType quantitationType, ExpressionDataMatrix<?> dmatrix)
static void	QuantitationTypeDetectionUtils.lintQuantitationType(QuantitationType quantitationType, ExpressionDataMatrix<?> dmatrix, boolean ignoreQuantitationMismatch)	Check if a given quantitation type adequately describes a given expression data matrix.

Uses of ExpressionDataMatrix in ubic.gemma.core.analysis.preprocess.filter

Classes in ubic.gemma.core.analysis.preprocess.filter with type parameters of type ExpressionDataMatrix

Modifier and Type	Interface	Description
interface	Filter<T extends ExpressionDataMatrix<?>>	Base interface for expression data filters.

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

Subinterfaces of ExpressionDataMatrix in ubic.gemma.core.datastructure.matrix

Modifier and Type	Interface	Description
interface	BulkExpressionDataMatrix<T>	Interface for bulk expression data matrices.
interface	BulkExpressionDataPrimitiveDoubleMatrix	Interface for bulk expression data matrices that can be efficiently accessed as a primitive double matrix.
interface	BulkExpressionDataPrimitiveIntMatrix	Interface for bulk expression data matrices that can be efficiently accessed as a primitive int matrix.
interface	ExpressionDataPrimitiveDoubleMatrix	Interface for matrices that can provide unboxed doubles.
interface	ExpressionDataPrimitiveIntMatrix
interface	MultiAssayBulkExpressionDataMatrix<T>	An interface for bulk matrices that supports multiple BioAssay per BioMaterial.
interface	SingleCellExpressionDataMatrix<T>	In a single-cell expression data matrix, each column represents a cell.

Classes in ubic.gemma.core.datastructure.matrix that implement ExpressionDataMatrix

Modifier and Type	Class	Description
class	AbstractBulkExpressionDataMatrix<T>	Base class for bulk expression data matrices.
class	AbstractExpressionDataMatrix<T>
class	AbstractMultiAssayExpressionDataMatrix<T>	Base class for ExpressionDataMatrix implementations that can deal with multiple BioAssays per BioMaterial.
class	AbstractSingleCellExpressionDataMatrix<T>
class	BulkExpressionDataDoubleMatrix
class	BulkExpressionDataIntMatrix	A bulk expression data matrix that can be efficiently accessed as a primitive int matrix.
class	EmptyBulkExpressionDataMatrix	An empty bulk expression data matrix.
class	EmptyExpressionMatrix	Used to make a 'dummy matrix' that has the column information populated.
class	EmptySingleCellExpressionDataMatrix
class	ExpressionDataBooleanMatrix	Matrix of booleans mapped from an ExpressionExperiment.
class	ExpressionDataDoubleMatrix	A data structure that holds a reference to the data for a given expression experiment.
class	ExpressionDataIntegerMatrix	Warning, not fully tested.
class	ExpressionDataStringMatrix
class	MaskedExpressionDataMatrix<T>	A wrapper for an ExpressionDataMatrix that applies a mask to the data, allowing selective access to the underlying matrix.
class	SingleCellExpressionDataDoubleMatrix
class	SingleCellExpressionDataIntMatrix

Methods in ubic.gemma.core.datastructure.matrix that return ExpressionDataMatrix

Modifier and Type	Method	Description
ExpressionDataMatrix<Double>	BulkExpressionDataDoubleMatrix.sliceRows(List<CompositeSequence> designElements)
ExpressionDataMatrix<Integer>	BulkExpressionDataIntMatrix.sliceRows(List<CompositeSequence> designElements)
ExpressionDataMatrix<Object>	EmptyBulkExpressionDataMatrix.sliceRows(List<CompositeSequence> designElements)
ExpressionDataMatrix<Object>	EmptyExpressionMatrix.sliceRows(List<CompositeSequence> designElements)
ExpressionDataMatrix<Object>	EmptySingleCellExpressionDataMatrix.sliceRows(List<CompositeSequence> designElements)
ExpressionDataMatrix<Boolean>	ExpressionDataBooleanMatrix.sliceRows(List<CompositeSequence> designElements)
ExpressionDataMatrix<Integer>	ExpressionDataIntegerMatrix.sliceRows(List<CompositeSequence> designElements)
ExpressionDataMatrix<T>	ExpressionDataMatrix.sliceRows(List<CompositeSequence> designElements)
ExpressionDataMatrix<String>	ExpressionDataStringMatrix.sliceRows(List<CompositeSequence> designElements)
ExpressionDataMatrix<T>	MaskedExpressionDataMatrix.sliceRows(List<CompositeSequence> designElements)
ExpressionDataMatrix<Double>	SingleCellExpressionDataDoubleMatrix.sliceRows(List<CompositeSequence> designElements)
ExpressionDataMatrix<Integer>	SingleCellExpressionDataIntMatrix.sliceRows(List<CompositeSequence> designElements)

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

Modifier and Type	Method	Description
static <T> MaskedExpressionDataMatrix<T>	MaskedExpressionDataMatrix.maskColumns(ExpressionDataMatrix<T> matrix, boolean[] columnMask, T maskedValue)	Mask whole columns of the given matrix.
static <T> MaskedExpressionDataMatrix<T>	MaskedExpressionDataMatrix.maskElements(ExpressionDataMatrix<T> matrix, boolean[][] mask, T maskedValue)	Mask individual elements of the given matrix.
static <T> MaskedExpressionDataMatrix<T>	MaskedExpressionDataMatrix.maskElements(ExpressionDataMatrix<T> matrix, int[] i, int[] j, T maskedValue)	Mask individual elements of the given matrix at the specified coordinates.
static <T> MaskedExpressionDataMatrix<T>	MaskedExpressionDataMatrix.maskRows(ExpressionDataMatrix<T> matrix, boolean[] rowMask, T maskedValue)	Mask whole rows of the given matrix.

Constructors in ubic.gemma.core.datastructure.matrix with parameters of type ExpressionDataMatrix

Modifier	Constructor	Description
	ExpressionDataMatrixRowElement(ExpressionDataMatrix<?> matrix, int i)

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

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

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