Package ubic.gemma.core.datastructure.matrix
@ParametersAreNonnullByDefault
package ubic.gemma.core.datastructure.matrix
This package contains data structures for representing matrices of gene expression.
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ClassDescriptionBase class for bulk expression data matrices.Base class for ExpressionDataMatrix implementations that can deal with multiple BioAssays per BioMaterial.A bulk expression data matrix that can be efficiently accessed as a primitive int matrix.Interface for bulk expression data matrices.Interface for bulk expression data matrices that can be efficiently accessed as a primitive double matrix.Interface for bulk expression data matrices that can be efficiently accessed as a primitive int matrix.An empty bulk expression data matrix.Used to make a 'dummy matrix' that has the column information populated.Matrix of booleans mapped from an ExpressionExperiment.A data structure that holds a reference to the data for a given expression experiment.Warning, not fully tested.Represents a matrix of data from an
ExpressionExperiment.Methods to organize ExpressionDataMatrices by column (or at least provide the ordering).Encapsulates information about the row 'label' for a ExpressionDataMatrix.Interface for matrices that can provide unboxed doubles.A wrapper for anExpressionDataMatrixthat applies a mask to the data, allowing selective access to the underlying matrix.An interface for bulk matrices that supports multipleBioAssayperBioMaterial.In a single-cell expression data matrix, each column represents a cell.Utility methods for taking an ExpressionExperiment and returning various types of ExpressionDataMatrices, such as the processed data, preferred data, background, etc.