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

Packages that use BulkExpressionDataMatrix

Package	Description
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.

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

Methods in ubic.gemma.core.analysis.singleCell.aggregate that return BulkExpressionDataMatrix

Modifier and Type	Method	Description
static <T> BulkExpressionDataMatrix<T>	SingleCellDataVectorAggregatorUtils.aggregate(SingleCellExpressionDataMatrix<T> scMatrix, SingleCellDataVectorAggregatorUtils.SingleCellAggregationMethod method, Class<T> scalarType)	Aggregate a single-cell data matrix.

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

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

Modifier and Type	Interface	Description
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	MultiAssayBulkExpressionDataMatrix<T>	An interface for bulk matrices that supports multiple BioAssay per BioMaterial.

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

Modifier and Type	Class	Description
class	AbstractBulkExpressionDataMatrix<T>	Base class for bulk expression data matrices.
class	AbstractMultiAssayExpressionDataMatrix<T>	Base class for ExpressionDataMatrix implementations that can deal with multiple BioAssays per BioMaterial.
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	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

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

Modifier and Type	Method	Description
static BulkExpressionDataMatrix<?>	BulkExpressionDataMatrix.getMatrix(Collection<? extends BulkExpressionDataVector> vectors)	Create a bulk expression data matrix from a collection of vectors.

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

Modifier and Type	Method	Description
static List<BioMaterial>	ExpressionDataMatrixColumnSort.orderByExperimentalDesign(BulkExpressionDataMatrix<?> dmatrix, Collection<ExperimentalFactor> factors, ExperimentalFactor primaryFactor)
static <T extends BulkExpressionDataVector> List<T>	BulkExpressionDataMatrixUtils.toVectors(BulkExpressionDataMatrix<?> matrix, Class<T> vectorType)	Convert a BulkExpressionDataMatrix to a collection of BulkExpressionDataVector.

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

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

Modifier and Type	Method	Description
int	JsonMatrixWriter.write(BulkExpressionDataMatrix<?> matrix, Class<? extends BulkExpressionDataVector> vectorType, Writer writer)
int	MatrixWriter.write(BulkExpressionDataMatrix<?> matrix, Class<? extends BulkExpressionDataVector> vectorType, Writer writer)
int	MatrixWriter.write(BulkExpressionDataMatrix<?> matrix, Class<? extends BulkExpressionDataVector> vectorType, Map<CompositeSequence,Collection<Gene>> geneAnnotations, Writer writer)
int	MatrixWriter.writeWithStringifiedGeneAnnotations(Writer writer, BulkExpressionDataMatrix<?> matrix, Class<? extends BulkExpressionDataVector> vectorType, Map<CompositeSequence,String[]> geneAnnotations)	Alternate method that uses annotations in string form (e.g., read from another file).