Uses of Class
ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVector

Packages that use SingleCellExpressionDataVector

Package	Description
ubic.gemma.core.analysis.singleCell	This package contains classes for analysing single-cell expression data.
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.
ubic.gemma.core.loader.expression.singleCell	This package contains classes for loading single cell expression data.
ubic.gemma.core.visualization
ubic.gemma.model.expression.bioAssayData
ubic.gemma.model.expression.experiment
ubic.gemma.persistence.service.expression.experiment

Uses of SingleCellExpressionDataVector in ubic.gemma.core.analysis.singleCell

Methods in ubic.gemma.core.analysis.singleCell that return types with arguments of type SingleCellExpressionDataVector

Modifier and Type	Method	Description
static Function<SingleCellExpressionDataVector,SingleCellExpressionDataVector>	SingleCellSlicerUtils.createSlicer(List<BioAssay> assays)	Create a slicer for single-cell data vectors.
static Function<SingleCellExpressionDataVector,SingleCellExpressionDataVector>	SingleCellSlicerUtils.createSlicer(List<BioAssay> assays)	Create a slicer for single-cell data vectors.
static Function<SingleCellExpressionDataVector,SingleCellExpressionDataVector>	SingleCellSlicerUtils.createSlicer(List<BioAssay> assays, List<String> cellIds, Set<CellTypeAssignment> ctas, Set<CellLevelCharacteristics> clcs)	Create a slicer for single-cell data vectors whose cell IDs, CTAs, and CLCs are already pre-sliced.
static Function<SingleCellExpressionDataVector,SingleCellExpressionDataVector>	SingleCellSlicerUtils.createSlicer(List<BioAssay> assays, List<String> cellIds, Set<CellTypeAssignment> ctas, Set<CellLevelCharacteristics> clcs)	Create a slicer for single-cell data vectors whose cell IDs, CTAs, and CLCs are already pre-sliced.
static Collection<SingleCellExpressionDataVector>	SingleCellSlicerUtils.slice(Collection<SingleCellExpressionDataVector> vectors, List<BioAssay> bioAssays)

Methods in ubic.gemma.core.analysis.singleCell with parameters of type SingleCellExpressionDataVector

Modifier and Type	Method	Description
void	SingleCellSparsityMetrics.addExpressedCells(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int characteristicIndex, boolean[] isExpressed)	Populate a boolean vector that indicates if a cell has at least one expressed gene.
static int[]	SingleCellDescriptive.count(SingleCellExpressionDataVector vector)	Count the number of values in each assay.
static int[]	SingleCellDescriptive.countAboveThreshold(SingleCellExpressionDataVector vector, double threshold)	Compute the number of cells expressed strictly above the given threshold.
static int[]	SingleCellDescriptive.countFast(SingleCellExpressionDataVector vector)	Quickly count the non-zeroes for each assay.
static int	SingleCellDescriptive.countFast(SingleCellExpressionDataVector vector, int sampleIndex)
static int	SingleCellDescriptive.countFast(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)
int	SingleCellSparsityMetrics.getNumberOfCellsByDesignElements(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int characteristicIndex)
int	SingleCellSparsityMetrics.getNumberOfDesignElements(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics characteristic, int characteristicIndex)
boolean	SingleCellSparsityMetrics.isSupported(SingleCellExpressionDataVector vector)	Check if sparsity metrics can be computed for a given collection of vectors.
static double[]	SingleCellDescriptive.max(SingleCellExpressionDataVector vector)
static double	SingleCellDescriptive.max(SingleCellExpressionDataVector vector, int sampleIndex)
static double	SingleCellDescriptive.max(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)
static double[][]	SingleCellDescriptive.max(SingleCellExpressionDataVector vector, CellLevelCharacteristics cellLevelCharacteristics)
static double[]	SingleCellDescriptive.mean(SingleCellExpressionDataVector vector)	Calculate the mean of each assay for a given vector.
static double	SingleCellDescriptive.mean(SingleCellExpressionDataVector vector, int sampleIndex)
static double	SingleCellDescriptive.mean(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)
static double	SingleCellDescriptive.mean(SingleCellExpressionDataVector vector, BioAssay sample)	Calculate the mean of a given assay.
static double[]	SingleCellDescriptive.median(SingleCellExpressionDataVector vector)	Calculate the median of each assay for a given vector.
static double	SingleCellDescriptive.median(SingleCellExpressionDataVector vector, int column)
static double	SingleCellDescriptive.median(SingleCellExpressionDataVector vector, int column, CellLevelCharacteristics cellLevelCharacteristics, int row)
static double[]	SingleCellDescriptive.min(SingleCellExpressionDataVector vector)
static double	SingleCellDescriptive.min(SingleCellExpressionDataVector vector, int sampleIndex)
static double	SingleCellDescriptive.min(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)
static double[][]	SingleCellDescriptive.min(SingleCellExpressionDataVector vector, CellLevelCharacteristics cellLevelCharacteristics)
static double[]	SingleCellDescriptive.quantile(SingleCellExpressionDataVector vector, double q)
static double	SingleCellDescriptive.quantile(SingleCellExpressionDataVector vector, int sampleIndex, double v)
static double	SingleCellDescriptive.quantile(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row, double q)
static double[]	SingleCellDescriptive.quantile(SingleCellExpressionDataVector vector, CellLevelCharacteristics cellLevelCharacteristics, int row, double q)
static double[]	SingleCellDescriptive.sampleStandardDeviation(SingleCellExpressionDataVector vector)
static double	SingleCellDescriptive.sampleStandardDeviation(SingleCellExpressionDataVector vector, BioAssay sample)
static double[]	SingleCellDescriptive.sampleVariance(SingleCellExpressionDataVector vector)
static double	SingleCellDescriptive.sampleVariance(SingleCellExpressionDataVector vector, BioAssay sample)	Calculate the variance of a given assay.
static double[]	SingleCellDescriptive.sum(SingleCellExpressionDataVector vector)
static double[][]	SingleCellDescriptive.sum(SingleCellExpressionDataVector vector, CellLevelCharacteristics cellLevelCharacteristics)
static double[]	SingleCellDescriptive.sumUnscaled(SingleCellExpressionDataVector vector)

Method parameters in ubic.gemma.core.analysis.singleCell with type arguments of type SingleCellExpressionDataVector

Modifier and Type	Method	Description
int	SingleCellSparsityMetrics.getNumberOfCells(Collection<SingleCellExpressionDataVector> vectors, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int characteristicIndex)	Calculate the number of cells with at least one gene expressed.
int	SingleCellSparsityMetrics.getNumberOfCellsByDesignElements(Collection<SingleCellExpressionDataVector> vectors, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int characteristicIndex)	Calculate the number of expressed cell by gene pairs.
int	SingleCellSparsityMetrics.getNumberOfDesignElements(Collection<SingleCellExpressionDataVector> vectors, int sampleIndex, CellLevelCharacteristics characteristic, int characteristicIndex)	Calculate the number of genes expressed in at least one cell.
static Collection<SingleCellExpressionDataVector>	SingleCellSlicerUtils.slice(Collection<SingleCellExpressionDataVector> vectors, List<BioAssay> bioAssays)

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

Methods in ubic.gemma.core.analysis.singleCell.aggregate that return types with arguments of type SingleCellExpressionDataVector

Modifier and Type	Method	Description
static Function<SingleCellExpressionDataVector,RawExpressionDataVector>	SingleCellDataVectorAggregatorUtils.createAggregator(SingleCellDataVectorAggregatorUtils.SingleCellAggregationMethod method, CellLevelCharacteristics cellLevelCharacteristics)	Create an aggregator that can be used on a Stream of vectors.

Method parameters in ubic.gemma.core.analysis.singleCell.aggregate with type arguments of type SingleCellExpressionDataVector

Modifier and Type	Method	Description
static Collection<RawExpressionDataVector>	SingleCellDataVectorAggregatorUtils.aggregate(Collection<SingleCellExpressionDataVector> vectors, SingleCellDataVectorAggregatorUtils.SingleCellAggregationMethod method, CellLevelCharacteristics cellLevelCharacteristics)	Aggregate a collection of vectors.

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

Constructor parameters in ubic.gemma.core.datastructure.matrix with type arguments of type SingleCellExpressionDataVector

Constructor	Description
SingleCellExpressionDataDoubleMatrix(Collection<SingleCellExpressionDataVector> vectors)
SingleCellExpressionDataIntMatrix(Collection<SingleCellExpressionDataVector> vectors)

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

Method parameters in ubic.gemma.core.datastructure.matrix.io with type arguments of type SingleCellExpressionDataVector

Modifier and Type	Method	Description
int	MexMatrixWriter.write(Stream<SingleCellExpressionDataVector> vectors, int numVecs, Map<BioAssay,Long> nnzBySample, Map<CompositeSequence,Set<Gene>> cs2gene, Path outputDir)	Writes a stream of vectors to a directory.
int	TabularMatrixWriter.write(Collection<SingleCellExpressionDataVector> vectors, Map<CompositeSequence,Set<Gene>> cs2gene, Writer writer)
int	TabularMatrixWriter.write(Stream<SingleCellExpressionDataVector> vectors, Map<CompositeSequence,Set<Gene>> cs2gene, Writer writer)

Uses of SingleCellExpressionDataVector in ubic.gemma.core.loader.expression.singleCell

Methods in ubic.gemma.core.loader.expression.singleCell that return types with arguments of type SingleCellExpressionDataVector

Modifier and Type	Method	Description
Stream<SingleCellExpressionDataVector>	AbstractDelegatingSingleCellDataLoader.loadVectors(Collection<CompositeSequence> designElements, SingleCellDimension dimension, QuantitationType quantitationType)
Stream<SingleCellExpressionDataVector>	AnnDataSingleCellDataLoader.loadVectors(Collection<CompositeSequence> designElements, SingleCellDimension dimension, QuantitationType quantitationType)
Stream<SingleCellExpressionDataVector>	MexSingleCellDataLoader.loadVectors(Collection<CompositeSequence> designElements, SingleCellDimension scd, QuantitationType quantitationType)
Stream<SingleCellExpressionDataVector>	NullSingleCellDataLoader.loadVectors(Collection<CompositeSequence> designElements, SingleCellDimension dimension, QuantitationType quantitationType)
Stream<SingleCellExpressionDataVector>	SingleCellDataLoader.loadVectors(Collection<CompositeSequence> designElements, SingleCellDimension dimension, QuantitationType quantitationType)	Produces a stream of single-cell expression data vectors for the given QuantitationType.

Uses of SingleCellExpressionDataVector in ubic.gemma.core.visualization

Constructors in ubic.gemma.core.visualization with parameters of type SingleCellExpressionDataVector

Constructor	Description
SingleCellDataBoxplot(SingleCellExpressionDataVector vector)

Uses of SingleCellExpressionDataVector in ubic.gemma.model.expression.bioAssayData

Methods in ubic.gemma.model.expression.bioAssayData that return types with arguments of type SingleCellExpressionDataVector

Modifier and Type	Method	Description
static Consumer<SingleCellExpressionDataVector>	SingleCellExpressionDataVectorUtils.createStreamMonitor(String logCategory, long numVecs)

Methods in ubic.gemma.model.expression.bioAssayData with parameters of type SingleCellExpressionDataVector

Modifier and Type	Method	Description
static double[]	SingleCellExpressionDataVectorUtils.getSampleDataAsDoubles(SingleCellExpressionDataVector vector, int sampleIndex)	Obtain the data of a sample.
static double[]	SingleCellExpressionDataVectorUtils.getSampleDataAsDoubles(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)	Obtain the data of a sample.
static double[]	SingleCellExpressionDataVectorUtils.getSampleDataAsDoubles(SingleCellExpressionDataVector vector, BioAssay sample)
static float[]	SingleCellExpressionDataVectorUtils.getSampleDataAsFloats(SingleCellExpressionDataVector vector, int sampleIndex)	Obtain the data of a sample.
static float[]	SingleCellExpressionDataVectorUtils.getSampleDataAsFloats(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)	Obtain the data of a sample.
static int[]	SingleCellExpressionDataVectorUtils.getSampleDataAsInts(SingleCellExpressionDataVector vector, int sampleIndex)
static int[]	SingleCellExpressionDataVectorUtils.getSampleDataAsInts(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)
static long[]	SingleCellExpressionDataVectorUtils.getSampleDataAsLongs(SingleCellExpressionDataVector vector, int sampleIndex)
static long[]	SingleCellExpressionDataVectorUtils.getSampleDataAsLongs(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)
static int	SingleCellExpressionDataVectorUtils.getSampleEnd(SingleCellExpressionDataVector vector, int sampleIndex, int after)	Get the *exclusive* index of the last cell for a given sample.
static int	SingleCellExpressionDataVectorUtils.getSampleEnd(SingleCellExpressionDataVector vector, BioAssay sample)
static int	SingleCellExpressionDataVectorUtils.getSampleEnd(SingleCellExpressionDataVector vector, BioAssay sample, int after)
static int	SingleCellExpressionDataVectorUtils.getSampleStart(SingleCellExpressionDataVector vector, int sampleIndex, int after)	Get the index of the first cell for a given sample.
static int	SingleCellExpressionDataVectorUtils.getSampleStart(SingleCellExpressionDataVector vector, BioAssay sample)
static int	SingleCellExpressionDataVectorUtils.getSampleStart(SingleCellExpressionDataVector vector, BioAssay sample, int after)

Uses of SingleCellExpressionDataVector in ubic.gemma.model.expression.experiment

Methods in ubic.gemma.model.expression.experiment that return types with arguments of type SingleCellExpressionDataVector

Modifier and Type	Method	Description
Set<SingleCellExpressionDataVector>	ExpressionExperiment.getSingleCellExpressionDataVectors()

Method parameters in ubic.gemma.model.expression.experiment with type arguments of type SingleCellExpressionDataVector

Modifier and Type	Method	Description
void	ExpressionExperiment.setSingleCellExpressionDataVectors(Set<SingleCellExpressionDataVector> singleCellExpressionDataVectors)

Uses of SingleCellExpressionDataVector in ubic.gemma.persistence.service.expression.experiment

Methods in ubic.gemma.persistence.service.expression.experiment that return SingleCellExpressionDataVector

Modifier and Type	Method	Description
SingleCellExpressionDataVector	ExpressionExperimentDao.getSingleCellDataVectorWithoutCellIds(ExpressionExperiment ee, QuantitationType quantitationType, CompositeSequence designElement)
SingleCellExpressionDataVector	ExpressionExperimentDaoImpl.getSingleCellDataVectorWithoutCellIds(ExpressionExperiment ee, QuantitationType quantitationType, CompositeSequence designElement)
SingleCellExpressionDataVector	SingleCellExpressionExperimentService.getSingleCellDataVectorWithoutCellIds(ExpressionExperiment ee, QuantitationType quantitationType, CompositeSequence designElement)	Obtain a single single-cell vector without initializing cell IDs.
SingleCellExpressionDataVector	SingleCellExpressionExperimentServiceImpl.getSingleCellDataVectorWithoutCellIds(ExpressionExperiment ee, QuantitationType quantitationType, CompositeSequence designElement)

Methods in ubic.gemma.persistence.service.expression.experiment that return types with arguments of type SingleCellExpressionDataVector

Modifier and Type	Method	Description
Optional<Collection<SingleCellExpressionDataVector>>	SingleCellExpressionExperimentService.getPreferredSingleCellDataVectors(ExpressionExperiment ee)	Obtain preferred single-cell vectors.
Optional<Collection<SingleCellExpressionDataVector>>	SingleCellExpressionExperimentServiceImpl.getPreferredSingleCellDataVectors(ExpressionExperiment ee)
List<SingleCellExpressionDataVector>	ExpressionExperimentDao.getSingleCellDataVectors(ExpressionExperiment expressionExperiment, QuantitationType quantitationType)	Obtain a set of single-cell data vectors for the given quantitation type.
List<SingleCellExpressionDataVector>	ExpressionExperimentDao.getSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, boolean includeCellIds, boolean includeData, boolean includeDataIndices)	Obtain a set of single-cell data vectors for the given quantitation type.
List<SingleCellExpressionDataVector>	ExpressionExperimentDaoImpl.getSingleCellDataVectors(ExpressionExperiment expressionExperiment, QuantitationType quantitationType)
List<SingleCellExpressionDataVector>	ExpressionExperimentDaoImpl.getSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, boolean includeCellIds, boolean includeData, boolean includeDataIndices)
Collection<SingleCellExpressionDataVector>	SingleCellExpressionExperimentService.getSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType)	Obtain single-cell vectors for a particular sample.
Collection<SingleCellExpressionDataVector>	SingleCellExpressionExperimentService.getSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)
Collection<SingleCellExpressionDataVector>	SingleCellExpressionExperimentService.getSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType)	Obtain single-cell vectors for a given quantitation type.
Collection<SingleCellExpressionDataVector>	SingleCellExpressionExperimentService.getSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)
Collection<SingleCellExpressionDataVector>	SingleCellExpressionExperimentServiceImpl.getSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType)
Collection<SingleCellExpressionDataVector>	SingleCellExpressionExperimentServiceImpl.getSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)
List<SingleCellExpressionDataVector>	SingleCellExpressionExperimentServiceImpl.getSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType)
Collection<SingleCellExpressionDataVector>	SingleCellExpressionExperimentServiceImpl.getSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)
Stream<SingleCellExpressionDataVector>	ExpressionExperimentDao.streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, boolean createNewSession)	Obtain a stream over the vectors for a given QT.
Stream<SingleCellExpressionDataVector>	ExpressionExperimentDao.streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, boolean createNewSession, boolean includeCellIds, boolean includeData, boolean includeDataIndices)
Stream<SingleCellExpressionDataVector>	ExpressionExperimentDaoImpl.streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, boolean createNewSession)
Stream<SingleCellExpressionDataVector>	ExpressionExperimentDaoImpl.streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, boolean createNewSession, boolean includeCellIds, boolean includeData, boolean includeDataIndices)
Stream<SingleCellExpressionDataVector>	SingleCellExpressionExperimentService.streamSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType, int fetchSize, boolean createNewSession)
Stream<SingleCellExpressionDataVector>	SingleCellExpressionExperimentService.streamSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType, int fetchSize, boolean createNewSession, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)
Stream<SingleCellExpressionDataVector>	SingleCellExpressionExperimentService.streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, boolean createNewSession)	Obtain a stream over single-cell vectors for a given quantitation type.
Stream<SingleCellExpressionDataVector>	SingleCellExpressionExperimentService.streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, boolean createNewSession, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)
Stream<SingleCellExpressionDataVector>	SingleCellExpressionExperimentServiceImpl.streamSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType, int fetchSize, boolean createNewSession)
Stream<SingleCellExpressionDataVector>	SingleCellExpressionExperimentServiceImpl.streamSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType, int fetchSize, boolean createNewSession, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)
Stream<SingleCellExpressionDataVector>	SingleCellExpressionExperimentServiceImpl.streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, boolean createNewSession)
Stream<SingleCellExpressionDataVector>	SingleCellExpressionExperimentServiceImpl.streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, boolean createNewSession, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)

Method parameters in ubic.gemma.persistence.service.expression.experiment with type arguments of type SingleCellExpressionDataVector

Modifier and Type	Method	Description
int	SingleCellExpressionExperimentService.addSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, Collection<SingleCellExpressionDataVector> vectors, String details)	Add single-cell data vectors.
int	SingleCellExpressionExperimentServiceImpl.addSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, Collection<SingleCellExpressionDataVector> vectors, String details)
int	SingleCellExpressionExperimentService.replaceSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, Collection<SingleCellExpressionDataVector> vectors, String details)	Replace existing single-cell data vectors for the given quantitation type.
int	SingleCellExpressionExperimentServiceImpl.replaceSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, Collection<SingleCellExpressionDataVector> vectors, String details)