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

Packages that use BulkExpressionDataMatrix

Package	Description
ubic.gemma.core.analysis.singleCell.aggregate	This packge contains classes for splitting 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

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

Modifier and Type	Class	Description
class	BaseExpressionDataMatrix<T>	Base class for ExpressionDataMatrix implementations.
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 matrix using all the vectors, which are assumed to all be of the same quantitation type.

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)

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
static String	ExpressionDataWriterUtils.constructSampleName(BulkExpressionDataMatrix<?> matrix, int assayColumnIndex)	Constructs a sample name for a given column of a data matrix.
default int	BulkExpressionDataMatrixWriter.write(BulkExpressionDataMatrix<?> matrix, OutputStream stream)
int	BulkExpressionDataMatrixWriter.write(BulkExpressionDataMatrix<?> matrix, Writer writer)
int	MatrixWriter.write(BulkExpressionDataMatrix<?> matrix, Writer writer)
int	MatrixWriter.write(BulkExpressionDataMatrix<?> matrix, Map<CompositeSequence,Collection<Gene>> geneAnnotations, Writer writer)
int	MatrixWriter.writeJSON(Writer writer, BulkExpressionDataMatrix<?> matrix)
int	MatrixWriter.writeWithStringifiedGeneAnnotations(Writer writer, BulkExpressionDataMatrix<?> matrix, Map<CompositeSequence,String[]> geneAnnotations)	Alternate method that uses annotations in string form (e.g., read from another file).