Uses of Class
ubic.gemma.core.util.matrix.DoubleMatrix

Packages that use DoubleMatrix

Package	Description
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.analysis.preprocess	This package contains classes for preprocessing expression data.
ubic.gemma.core.analysis.preprocess.normalize
ubic.gemma.core.analysis.preprocess.svd
ubic.gemma.core.analysis.service
ubic.gemma.core.datastructure.matrix	This package contains data structures for representing matrices of gene expression.
ubic.gemma.core.loader.expression	This package contains interfaces and classes for loading expression data.
ubic.gemma.core.loader.expression.simple
ubic.gemma.core.ontology
ubic.gemma.core.util
ubic.gemma.core.util.graphics
ubic.gemma.core.util.math
ubic.gemma.core.util.math.linalg
ubic.gemma.core.util.math.linearmodels
ubic.gemma.core.util.matrix	Labelled-axis matrix types ported in-tree from baseCode's ubic.basecode.dataStructure.matrix subsystem as part of the Phase 3 baseCode retirement (see BASECODE_MATRIX_RECCE.md and BASECODE_DEP_AUDIT.md).
ubic.gemma.persistence.service.analysis.expression.pca
ubic.gemma.persistence.service.analysis.expression.sampleCoexpression
ubic.gemma.rest

Uses of DoubleMatrix in ubic.gemma.core.analysis.expression.diff

Methods in ubic.gemma.core.analysis.expression.diff that return DoubleMatrix

Modifier and Type	Method	Description
static DoubleMatrix<String,String>	DiffExAnalyzerUtils.makeDataMatrix(ObjectMatrix<String,String,Object> designMatrix, DoubleMatrix<CompositeSequence, BioMaterial> namedMatrix)	Convert the data into a string-keyed matrix.

Methods in ubic.gemma.core.analysis.expression.diff with parameters of type DoubleMatrix

Modifier and Type	Method	Description
static DoubleMatrix<String,String>	DiffExAnalyzerUtils.makeDataMatrix(ObjectMatrix<String,String,Object> designMatrix, DoubleMatrix<CompositeSequence, BioMaterial> namedMatrix)	Convert the data into a string-keyed matrix.

Uses of DoubleMatrix in ubic.gemma.core.analysis.preprocess

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

Modifier and Type	Method	Description
Collection<OutlierDetails>	OutlierDetectionService.identifyOutliersByMedianCorrelation(DoubleMatrix<BioAssay,BioAssay> cormat)	Identify outliers by sorting by median, then looking for non-overlap of first quartile-second quartile range This is exposed for efficiency in geeq score calculation, use this#identifyOutliers(ExpressionExperiment, boolean, boolean) to have the correlation matrix computed correctly for you.
Collection<OutlierDetails>	OutlierDetectionServiceImpl.identifyOutliersByMedianCorrelation(DoubleMatrix<BioAssay,BioAssay> cormat)

Uses of DoubleMatrix in ubic.gemma.core.analysis.preprocess.normalize

Methods in ubic.gemma.core.analysis.preprocess.normalize that return DoubleMatrix

Modifier and Type	Method	Description
DoubleMatrix<R,C>	QuantileNormalizer.normalize(DoubleMatrix<R,C> dataMatrix)
DoubleMatrix<R,C>	QuantileNormalizer.normalize(DoubleMatrix<R,C> dataMatrix, boolean[] includeInReference)	Normalize, letting only some columns define the reference distribution.

Methods in ubic.gemma.core.analysis.preprocess.normalize with parameters of type DoubleMatrix

Modifier and Type	Method	Description
DoubleMatrix<R,C>	QuantileNormalizer.normalize(DoubleMatrix<R,C> dataMatrix)
DoubleMatrix<R,C>	QuantileNormalizer.normalize(DoubleMatrix<R,C> dataMatrix, boolean[] includeInReference)	Normalize, letting only some columns define the reference distribution.

Uses of DoubleMatrix in ubic.gemma.core.analysis.preprocess.svd

Methods in ubic.gemma.core.analysis.preprocess.svd that return DoubleMatrix

Modifier and Type	Method	Description
DoubleMatrix<Integer,Integer>	ExpressionDataSVD.getS()
DoubleMatrix<CompositeSequence, Integer>	ExpressionDataSVD.getU()
DoubleMatrix<Integer, BioMaterial>	ExpressionDataSVD.getV()
DoubleMatrix<BioMaterial, Integer>	SVDResult.getVMatrix()	Row names: biomaterials; column names: eigengene number (from 0)

Uses of DoubleMatrix in ubic.gemma.core.analysis.service

Methods in ubic.gemma.core.analysis.service that return DoubleMatrix

Modifier and Type	Method	Description
DoubleMatrix<Gene, ExpressionExperiment>	ExpressionDataMatrixService.getRankMatrix(Collection<Gene> genes, Collection<ExpressionExperiment> ees, ProcessedExpressionDataVectorDao.RankMethod method)
DoubleMatrix<Gene, ExpressionExperiment>	ExpressionDataMatrixServiceImpl.getRankMatrix(Collection<Gene> genes, Collection<ExpressionExperiment> ees, ProcessedExpressionDataVectorDao.RankMethod method)

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

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

Modifier and Type	Method	Description
DoubleMatrix<CompositeSequence, BioMaterial>	ExpressionDataDoubleMatrix.getMatrix()
static <R> DoubleMatrix<R,BioAssay>	ExpressionDataMatrixColumnSort.orderByExperimentalDesign(DoubleMatrix<R,BioAssay> mat, Collection<ExperimentalFactor> factors, ExperimentalFactor primaryFactor)

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

Modifier and Type	Method	Description
static <R> DoubleMatrix<R,BioAssay>	ExpressionDataMatrixColumnSort.orderByExperimentalDesign(DoubleMatrix<R,BioAssay> mat, Collection<ExperimentalFactor> factors, ExperimentalFactor primaryFactor)
ExpressionDataDoubleMatrix	ExpressionDataDoubleMatrix.withMatrix(DoubleMatrix<CompositeSequence, BioMaterial> matrix)	Create a copy of this matrix with the given data matrix.
ExpressionDataDoubleMatrix	ExpressionDataDoubleMatrix.withMatrix(DoubleMatrix<CompositeSequence, BioMaterial> matrix, Map<QuantitationType, QuantitationType> quantitationTypes)	Create a copy of this matrix with the given data matrix and quantitation types.

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

Modifier	Constructor	Description
	ExpressionDataDoubleMatrix(ExpressionExperiment ee, DoubleMatrix<CompositeSequence, BioMaterial> dataMatrix, QuantitationType qt)	Create a matrix given a 'raw' matrix that uses the same samples as the experiment.

Uses of DoubleMatrix in ubic.gemma.core.loader.expression

Methods in ubic.gemma.core.loader.expression with parameters of type DoubleMatrix

Modifier and Type	Method	Description
void	DataUpdater.addCountData(ExpressionExperiment ee, ArrayDesign targetArrayDesign, DoubleMatrix<String,String> countMatrix, DoubleMatrix<String,String> rpkmMatrix, Map<BioAssay, SequencingMetadata> sequencingMetadata, boolean allowMissingSamples)
void	DataUpdaterImpl.addCountData(ExpressionExperiment ee, ArrayDesign targetArrayDesign, DoubleMatrix<String,String> countMatrix, DoubleMatrix<String,String> rpkmMatrix, Map<BioAssay, SequencingMetadata> sequencingMetadata, boolean allowMissingSamples)	RNA-seq: Replaces data.
void	DataUpdater.replaceData(ExpressionExperiment ee, ArrayDesign targetPlatform, QuantitationType qt, DoubleMatrix<String,String> data)
void	DataUpdaterImpl.replaceData(ExpressionExperiment ee, ArrayDesign targetPlatform, QuantitationType qt, DoubleMatrix<String,String> data)	Replace the data associated with the experiment (or add it if there is none).

Uses of DoubleMatrix in ubic.gemma.core.loader.expression.simple

Methods in ubic.gemma.core.loader.expression.simple with parameters of type DoubleMatrix

Modifier and Type	Method	Description
ExpressionExperiment	SimpleExpressionDataLoaderService.convert(SimpleExpressionExperimentMetadata metaData, DoubleMatrix<String,String> data)	Convert simple experiment metadata and data into Gemma objects.
ExpressionExperiment	SimpleExpressionDataLoaderServiceImpl.convert(SimpleExpressionExperimentMetadata metaData, DoubleMatrix<String,String> matrix)
ExpressionExperiment	SimpleExpressionDataLoaderService.create(SimpleExpressionExperimentMetadata metaData, DoubleMatrix<String,String> data)	Parses, converts (into Gemma objects), and loads data into the database.
ExpressionExperiment	SimpleExpressionDataLoaderServiceImpl.create(SimpleExpressionExperimentMetadata metaData, DoubleMatrix<String,String> matrix)

Uses of DoubleMatrix in ubic.gemma.core.ontology

Methods in ubic.gemma.core.ontology that return DoubleMatrix

Modifier and Type	Method	Description
DoubleMatrix<Long,String>	GoMetric.createVectorMatrix(Map<Long, Collection<String>> gene2go, boolean weight)
DoubleMatrix<Long,String>	GoMetricImpl.createVectorMatrix(Map<Long, Collection<String>> gene2go, boolean weight)

Methods in ubic.gemma.core.ontology with parameters of type DoubleMatrix

Modifier and Type	Method	Description
Double	GoMetric.computeMatrixSimilarity(Gene gene1, Gene gene2, DoubleMatrix<Long,String> gene2TermMatrix, GoMetric.Metric metric)
Double	GoMetricImpl.computeMatrixSimilarity(Gene gene1, Gene gene2, DoubleMatrix<Long,String> gene2TermMatrix, GoMetric.Metric metric)

Uses of DoubleMatrix in ubic.gemma.core.util

Methods in ubic.gemma.core.util with parameters of type DoubleMatrix

Modifier and Type	Method	Description
static DoubleMatrix2D	MatrixStats.ranksByColumn(DoubleMatrix<?,?> dmatrix)	Calculate the ranks of each value in each column of the matrix.
static DoubleMatrix1D	MatrixStats.rowMeans(DoubleMatrix<?,?> dmatrix)	Return the mean of each row in the matrix.

Uses of DoubleMatrix in ubic.gemma.core.util.graphics

Fields in ubic.gemma.core.util.graphics declared as DoubleMatrix

Modifier and Type	Field	Description
protected DoubleMatrix<A,B>	ColorMatrix.maxtrix

Methods in ubic.gemma.core.util.graphics that return DoubleMatrix

Modifier and Type	Method	Description
DoubleMatrix<A,B>	ColorMatrix.getMatrix()
DoubleMatrix<R,C>	MatrixDisplay.getMatrix()
DoubleMatrix<A,B>	ColorMatrix.getMaxtrix()

Methods in ubic.gemma.core.util.graphics with parameters of type DoubleMatrix

Modifier and Type	Method	Description
static <R,C> ColorMatrix<R,C>	ColorMatrix.newInstance(DoubleMatrix<R,C> matrix)

Constructors in ubic.gemma.core.util.graphics with parameters of type DoubleMatrix

Modifier	Constructor	Description
	ColorMatrix(DoubleMatrix<A,B> matrix)
	ColorMatrix(DoubleMatrix<A,B> matrix, Color[] colorMap, Color missingColor)
	MatrixDisplay(DoubleMatrix<R,C> matrix)

Uses of DoubleMatrix in ubic.gemma.core.util.math

Methods in ubic.gemma.core.util.math that return DoubleMatrix

Modifier and Type	Method	Description
static <R,C> DoubleMatrix<R,C>	MatrixStats.convertToLog2Cpm(DoubleMatrix<R,C> matrix, DoubleMatrix1D librarySize)	Convert a count matrix to log2 counts per million.
static <R,C> DoubleMatrix<R,R>	MatrixStats.correlationMatrix(DoubleMatrix<R,C> data)	Compute the correlation matrix of the rows of a matrix.
static <R,C> DoubleMatrix<R,C>	MatrixStats.doubleStandardize(DoubleMatrix<R,C> matrix)	Iteratively standardize the columns and rows of the matrix.
DoubleMatrix<R,C>	MatrixNormalizer.quantileNormalize(DoubleMatrix<R,C> matrix)	Rows with all missing will not be returned.
DoubleMatrix<R,C>	MatrixNormalizer.quantileNormalize(DoubleMatrix<R,C> matrix, boolean[] includeInReference)	Quantile-normalize, optionally computing the reference distribution from a subset of the columns.
static <R,C> DoubleMatrix<R,C>	MatrixStats.standardize(DoubleMatrix<R,C> matrix)	Scale the rows of the matrix; returns a new matrix.

Methods in ubic.gemma.core.util.math with parameters of type DoubleMatrix

Modifier and Type	Method	Description
static <R,C> DoubleMatrix1D	MatrixStats.colSums(DoubleMatrix<R,C> data)	NaN values are omitted from calculations.
static <R,C> void	MatrixStats.convertToLog2(DoubleMatrix<R,C> matrix, double base)	Convert a log_b-transformed data set to log 2.
static <R,C> DoubleMatrix<R,C>	MatrixStats.convertToLog2Cpm(DoubleMatrix<R,C> matrix, DoubleMatrix1D librarySize)	Convert a count matrix to log2 counts per million.
static <R,C> DoubleMatrix<R,R>	MatrixStats.correlationMatrix(DoubleMatrix<R,C> data)	Compute the correlation matrix of the rows of a matrix.
static <R,C> SparseDoubleMatrix<R,R>	MatrixStats.correlationMatrix(DoubleMatrix<R,C> data, double threshold)
static <R,C> DoubleMatrix<R,C>	MatrixStats.doubleStandardize(DoubleMatrix<R,C> matrix)	Iteratively standardize the columns and rows of the matrix.
static <R,C> void	MatrixStats.logTransform(DoubleMatrix<R,C> matrix)	Log-transform the values in a matrix (log base 2).
static <R,C> double	MatrixStats.max(DoubleMatrix<R,C> matrix)	Compute the maximum value in the matrix.
static <R,C> DoubleArrayList	MatrixRowStats.means(DoubleMatrix<R,C> M)	Calculates the means of a matrix's rows.
static <R,C> double	MatrixStats.min(DoubleMatrix<R,C> matrix)	Find the minimum of the entire matrix.
DoubleMatrix<R,C>	MatrixNormalizer.quantileNormalize(DoubleMatrix<R,C> matrix)	Rows with all missing will not be returned.
DoubleMatrix<R,C>	MatrixNormalizer.quantileNormalize(DoubleMatrix<R,C> matrix, boolean[] includeInReference)	Quantile-normalize, optionally computing the reference distribution from a subset of the columns.
static <R,C> void	MatrixStats.rbfNormalize(DoubleMatrix<R,C> matrixToNormalize, double sigma)	Normalize a matrix in place to be a transition matrix.
static <R,C> DoubleArrayList	MatrixRowStats.sampleStandardDeviations(DoubleMatrix<R,C> M)	Calculates the sample standard deviation of each row of a matrix
static <R,C> DoubleMatrix<R,C>	MatrixStats.standardize(DoubleMatrix<R,C> matrix)	Scale the rows of the matrix; returns a new matrix.
static <R,C> DoubleArrayList	MatrixRowStats.sumOfSquares(DoubleMatrix<R,C> M)	Calculates the sum of squares for each row of a matrix
static <R,C> DoubleArrayList	MatrixRowStats.sums(DoubleMatrix<R,C> M)	Calculate the sums of a matrix's rows.
static <R,C> void	MatrixStats.unLogTransform(DoubleMatrix<R,C> matrix)	Undo log2 transform.

Uses of DoubleMatrix in ubic.gemma.core.util.math.linalg

Methods in ubic.gemma.core.util.math.linalg that return DoubleMatrix

Modifier and Type	Method	Description
DoubleMatrix<Integer,Integer>	SingularValueDecomposition.getS()
DoubleMatrix<R,Integer>	SingularValueDecomposition.getU()
DoubleMatrix<Integer,C>	SingularValueDecomposition.getV()

Constructors in ubic.gemma.core.util.math.linalg with parameters of type DoubleMatrix

Modifier	Constructor	Description
	SingularValueDecomposition(DoubleMatrix<R,C> matrix)

Uses of DoubleMatrix in ubic.gemma.core.util.math.linearmodels

Methods in ubic.gemma.core.util.math.linearmodels that return DoubleMatrix

Modifier and Type	Method	Description
DoubleMatrix<String,String>	LinearModelSummary.getContrastCoefficients()
DoubleMatrix<String,String>	DesignMatrix.getMatrix()

Methods in ubic.gemma.core.util.math.linearmodels with parameters of type DoubleMatrix

Modifier and Type	Method	Description
static Map<String, Collection<String>>	LinearModelSummaryUtils.createTerm2CoefficientNames(List<String> factorNames, DoubleMatrix<String,String> contrastCoefficients)

Constructors in ubic.gemma.core.util.math.linearmodels with parameters of type DoubleMatrix

Modifier	Constructor	Description
	LeastSquaresFit(DesignMatrix designMatrix, DoubleMatrix<String,String> data)	Preferred interface if you want control over how the design is set up.
	LeastSquaresFit(DesignMatrix designMatrix, DoubleMatrix<String,String> data, DoubleMatrix2D weights)	Weighted least squares fit between two matrices
	LeastSquaresFit(ObjectMatrix<String,String,Object> design, DoubleMatrix<String,String> b)	NamedMatrix allows easier handling of the results.
	LeastSquaresFit(ObjectMatrix<String,String,Object> design, DoubleMatrix<String,String> data, boolean interactions)	NamedMatrix allows easier handling of the results.
	MeanVarianceEstimator(DesignMatrix designMatrix, DoubleMatrix<String,String> data, DoubleMatrix1D librarySize)	Preferred interface if you want control over how the design is set up.

Uses of DoubleMatrix in ubic.gemma.core.util.matrix

Subclasses of DoubleMatrix in ubic.gemma.core.util.matrix

Modifier and Type	Class	Description
class	CompressedSparseDoubleMatrix<R,C>	Supports sparse matrices (where sparse means most values are zero, not that they are missing).
class	DenseDoubleMatrix<R,C>	A dense matrix of doubles that knows about row and column names.
class	FastRowAccessDoubleMatrix<R,C>	Dense 2D matrix implementation designed for very fast access of entire rows.
class	SparseDoubleMatrix<R,C>	A sparse matrix that knows about row and column names.

Subclasses with type arguments of type DoubleMatrix in ubic.gemma.core.util.matrix

Modifier and Type	Class	Description
class	DoubleMatrixReader	Reader for DoubleMatrix.

Methods in ubic.gemma.core.util.matrix that return DoubleMatrix

Modifier and Type	Method	Description
DoubleMatrix<R,C>	CompressedSparseDoubleMatrix.copy()
DoubleMatrix<R,C>	DenseDoubleMatrix.copy()
abstract DoubleMatrix<R,C>	DoubleMatrix.copy()	Create a deep copy of this
DoubleMatrix<R,C>	FastRowAccessDoubleMatrix.copy()
DoubleMatrix<R,C>	SparseDoubleMatrix.copy()
protected DoubleMatrix<String,String>	DoubleMatrixReader.createMatrix(List<DoubleArrayList> MTemp, List<String> rowNames, List<String> colNames1)
DoubleMatrix<R,C>	CompressedSparseDoubleMatrix.getColRange(int startCol, int endCol)
DoubleMatrix<R,C>	DenseDoubleMatrix.getColRange(int startCol, int endCol)
abstract DoubleMatrix<R,C>	DoubleMatrix.getColRange(int startCol, int endCol)
DoubleMatrix<R,C>	FastRowAccessDoubleMatrix.getColRange(int startCol, int endCol)
DoubleMatrix<R,C>	SparseDoubleMatrix.getColRange(int startCol, int endCol)
DoubleMatrix<R,C>	CompressedSparseDoubleMatrix.getRowRange(int startRow, int endRow)
DoubleMatrix<R,C>	DenseDoubleMatrix.getRowRange(int startRow, int endRow)
abstract DoubleMatrix<R,C>	DoubleMatrix.getRowRange(int startRow, int endRow)
DoubleMatrix<R,C>	FastRowAccessDoubleMatrix.getRowRange(int startRow, int endRow)
DoubleMatrix<R,C>	SparseDoubleMatrix.getRowRange(int startRow, int endRow)
DoubleMatrix<String,String>	DoubleMatrixReader.read(InputStream stream)
DoubleMatrix<String,String>	DoubleMatrixReader.read(InputStream stream, Collection<String> wantedRowNames)
DoubleMatrix<String,String>	DoubleMatrixReader.read(InputStream stream, Collection<String> wantedRowNames, boolean createEmptyRows, int skipColumns, int maxRows)
DoubleMatrix<String,String>	DoubleMatrixReader.read(InputStream stream, Collection<String> wantedRowNames, int numberOfColumnsToSkip)
DoubleMatrix<String,String>	DoubleMatrixReader.read(String filename)
DoubleMatrix<String,String>	DoubleMatrixReader.read(String filename, int maxRows)
DoubleMatrix<String,String>	DoubleMatrixReader.read(String filename, Collection<String> wantedRowNames)	Read a matrix from a file, subject to filtering criteria.
DoubleMatrix<String,String>	DoubleMatrixReader.read(String fileName, Collection<String> wantedRowNames, int numberOfColumnsToSkip)
DoubleMatrix<R,C>	CompressedSparseDoubleMatrix.subsetColumns(List<C> columns)
DoubleMatrix<R,C>	DenseDoubleMatrix.subsetColumns(List<C> columns)
abstract DoubleMatrix<R,C>	DoubleMatrix.subsetColumns(List<C> columns)	Create a copy of this matrix with only the selected columns, in the selected order.
DoubleMatrix<R,C>	FastRowAccessDoubleMatrix.subsetColumns(List<C> columns)
DoubleMatrix<R,C>	SparseDoubleMatrix.subsetColumns(List<C> columns)
DoubleMatrix<R,C>	CompressedSparseDoubleMatrix.subsetRows(List<R> rowNames)
DoubleMatrix<R,C>	DenseDoubleMatrix.subsetRows(List<R> rowNames)
abstract DoubleMatrix<R,C>	DoubleMatrix.subsetRows(List<R> rowNames)	Create a copy of this matrix with only the selected rows, in the selected order.
DoubleMatrix<R,C>	FastRowAccessDoubleMatrix.subsetRows(List<R> rowNames)
DoubleMatrix<R,C>	SparseDoubleMatrix.subsetRows(List<R> rowNames)
DoubleMatrix<C,R>	CompressedSparseDoubleMatrix.transpose()
DoubleMatrix<C,R>	DenseDoubleMatrix.transpose()
abstract DoubleMatrix<C,R>	DoubleMatrix.transpose()
DoubleMatrix<C,R>	FastRowAccessDoubleMatrix.transpose()
DoubleMatrix<C,R>	SparseDoubleMatrix.transpose()

Methods in ubic.gemma.core.util.matrix with parameters of type DoubleMatrix

Modifier and Type	Method	Description
static DenseDoubleMatrix<String,String>	DoubleMatrixFactory.dense(DoubleMatrix<String,String> T)	Creates a matrix in which the underlying data is a copy; the row and column labels are not copied.

Uses of DoubleMatrix in ubic.gemma.persistence.service.analysis.expression.pca

Methods in ubic.gemma.persistence.service.analysis.expression.pca with parameters of type DoubleMatrix

Modifier and Type	Method	Description
PrincipalComponentAnalysis	PrincipalComponentAnalysisService.create(ExpressionExperiment ee, DoubleMatrix<CompositeSequence, Integer> u, double[] eigenvalues, DoubleMatrix<Integer, BioMaterial> v, BioAssayDimension bad, int numComponentsToStore, int numLoadingsToStore)
PrincipalComponentAnalysis	PrincipalComponentAnalysisServiceImpl.create(ExpressionExperiment ee, DoubleMatrix<CompositeSequence, Integer> u, double[] eigenvalues, DoubleMatrix<Integer, BioMaterial> v, BioAssayDimension bad, int numComponentsToStore, int numLoadingsToStore)

Uses of DoubleMatrix in ubic.gemma.persistence.service.analysis.expression.sampleCoexpression

Methods in ubic.gemma.persistence.service.analysis.expression.sampleCoexpression that return DoubleMatrix

Modifier and Type	Method	Description
DoubleMatrix<BioAssay,BioAssay>	SampleCoexpressionAnalysisService.compute(ExpressionExperiment ee, PreparedCoexMatrices matrices)	Computes sample correlation matrices for the given experiment.
DoubleMatrix<BioAssay,BioAssay>	SampleCoexpressionAnalysisServiceImpl.compute(ExpressionExperiment ee, PreparedCoexMatrices matrices)	Unfortunately, this method breaks under high contention (see #400, so we need to fully lock the database while undergoing using Isolation.SERIALIZABLE transaction isolation level.
DoubleMatrix<BioAssay,BioAssay>	SampleCoexpressionAnalysisService.loadBestMatrix(ExpressionExperiment ee)	Loads the analysis containing the coexpression matrices for the given experiment and converts the regressed coexpression matrix into a double matrix.
DoubleMatrix<BioAssay,BioAssay>	SampleCoexpressionAnalysisServiceImpl.loadBestMatrix(ExpressionExperiment ee)
DoubleMatrix<BioAssay,BioAssay>	SampleCoexpressionAnalysisService.loadFullMatrix(ExpressionExperiment ee)	Loads the analysis containing the coexpression matrices for the given experiment and converts the full (non-regressed) coexpression matrix into a double matrix.
DoubleMatrix<BioAssay,BioAssay>	SampleCoexpressionAnalysisServiceImpl.loadFullMatrix(ExpressionExperiment ee)
DoubleMatrix<BioAssay,BioAssay>	SampleCoexpressionAnalysisService.loadRegressedMatrix(ExpressionExperiment ee)	Load the regressed coexpression matrix for the given experiment.
DoubleMatrix<BioAssay,BioAssay>	SampleCoexpressionAnalysisServiceImpl.loadRegressedMatrix(ExpressionExperiment ee)
DoubleMatrix<BioAssay,BioAssay>	SampleCoexpressionAnalysisService.retrieveExisting(ExpressionExperiment ee)
DoubleMatrix<BioAssay,BioAssay>	SampleCoexpressionAnalysisServiceImpl.retrieveExisting(ExpressionExperiment ee)

Uses of DoubleMatrix in ubic.gemma.rest

Constructors in ubic.gemma.rest with parameters of type DoubleMatrix

Modifier	Constructor	Description
	SampleCorrelationMatrixValueObject(DoubleMatrix<BioAssay,BioAssay> matrix, String matrixKind, Set<Long> actualOutlierIds, Set<Long> predictedOutlierIds)