Uses of Class
ubic.gemma.model.expression.bioAssay.BioAssay

Packages that use BioAssay

Package	Description
ubic.gemma.cli.util
ubic.gemma.core.analysis.preprocess	This package contains classes for preprocessing expression data.
ubic.gemma.core.analysis.preprocess.batcheffects
ubic.gemma.core.analysis.preprocess.slice	This package provides capabilities for slicing BulkExpressionDataVector.
ubic.gemma.core.analysis.preprocess.svd
ubic.gemma.core.analysis.service
ubic.gemma.core.analysis.singleCell	This package contains classes for analysing single-cell expression data.
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.
ubic.gemma.core.loader.expression	This package contains interfaces and classes for loading expression data.
ubic.gemma.core.loader.expression.arrayDesign
ubic.gemma.core.loader.expression.geo.singleCell	This package contains specific logic for dealing with single-cell data from GEO.
ubic.gemma.core.loader.expression.sequencing	This package contains interfaces and classes for loading sequencing data.
ubic.gemma.core.loader.expression.singleCell	This package contains classes for loading single-cell expression data.
ubic.gemma.core.loader.util.mapper	Utilities for mapping Identifiable entities to external identifiers.
ubic.gemma.core.visualization
ubic.gemma.core.visualization.cellbrowser	This package contains classes related to the Cell Browser visualization tool.
ubic.gemma.model.expression.bioAssay
ubic.gemma.model.expression.bioAssayData
ubic.gemma.model.expression.biomaterial
ubic.gemma.model.expression.experiment
ubic.gemma.persistence.service.analysis.expression.sampleCoexpression
ubic.gemma.persistence.service.expression.arrayDesign
ubic.gemma.persistence.service.expression.bioAssay
ubic.gemma.persistence.service.expression.bioAssayData
ubic.gemma.persistence.service.expression.biomaterial
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.util

Uses of BioAssay in ubic.gemma.cli.util

Methods in ubic.gemma.cli.util that return BioAssay

Modifier and Type	Method	Description
BioAssay	EntityLocator.locateBioAssay(ExpressionExperiment ee, String sampleId)
BioAssay	EntityLocator.locateBioAssay(ExpressionExperiment ee, QuantitationType quantitationType, String sampleId)
BioAssay	EntityLocatorImpl.locateBioAssay(ExpressionExperiment ee, String sampleId)
BioAssay	EntityLocatorImpl.locateBioAssay(ExpressionExperiment ee, QuantitationType qt, String sampleId)

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

Method parameters in ubic.gemma.core.analysis.preprocess with type arguments of type BioAssay

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>	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)
Collection<OutlierDetails>	OutlierDetectionServiceImpl.identifyOutliersByMedianCorrelation(DoubleMatrix<BioAssay,BioAssay> cormat)

Uses of BioAssay in ubic.gemma.core.analysis.preprocess.batcheffects

Methods in ubic.gemma.core.analysis.preprocess.batcheffects that return types with arguments of type BioAssay

Modifier and Type	Method	Description
static Map<String,BioAssay>	BatchInfoParser.getAccessionToBioAssayMap(ExpressionExperiment ee)

Uses of BioAssay in ubic.gemma.core.analysis.preprocess.slice

Method parameters in ubic.gemma.core.analysis.preprocess.slice with type arguments of type BioAssay

Modifier and Type	Method	Description
static <T extends BulkExpressionDataVector> Function<T,T>	BulkDataSlicerUtils.createSlicer(List<BioAssay> assays, Class<T> vectorType)	Create a slicer function for bulk data vectors that can be applied on a Stream.
static <T extends BulkExpressionDataVector> Collection<T>	BulkDataSlicerUtils.slice(Collection<T> vectors, List<BioAssay> assays, Class<T> vectorType)	Slice a collection of bulk data vectors.

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

Methods in ubic.gemma.core.analysis.preprocess.svd that return types with arguments of type BioAssay

Modifier and Type	Method	Description
List<BioAssay>	SVDResult.getBioAssays()	Assays used in the SVD analysis.

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

Methods in ubic.gemma.core.analysis.service with parameters of type BioAssay

Modifier and Type	Method	Description
static String	ExpressionDataFileUtils.formatBioAssayFilename(BioAssay ba)

Method parameters in ubic.gemma.core.analysis.service with type arguments of type BioAssay

Modifier and Type	Method	Description
static String	ExpressionDataFileUtils.getDataOutputFilename(ExpressionExperiment ee, List<BioAssay> assays, boolean filtered, String suffix)
static String	ExpressionDataFileUtils.getDataOutputFilename(ExpressionExperiment ee, List<BioAssay> assays, QuantitationType type, String suffix)	Obtain the filename for writing a specific QT.
ExpressionDataDoubleMatrix	ExpressionDataMatrixService.getProcessedExpressionDataMatrix(ExpressionExperiment ee, List<BioAssay> samples)
ExpressionDataDoubleMatrix	ExpressionDataMatrixServiceImpl.getProcessedExpressionDataMatrix(ExpressionExperiment ee, List<BioAssay> samples)
ExpressionDataDoubleMatrix	ExpressionDataMatrixService.getRawExpressionDataMatrix(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType)
ExpressionDataDoubleMatrix	ExpressionDataMatrixServiceImpl.getRawExpressionDataMatrix(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType)
void	OutlierFlaggingService.markAsMissing(Collection<BioAssay> assaysToRemove)	This does not actually remove the sample; rather, it sets all values to "missing" in the processed data.
void	OutlierFlaggingServiceImpl.markAsMissing(Collection<BioAssay> bioAssays)
void	OutlierFlaggingService.unmarkAsMissing(Collection<BioAssay> bioAssays)	Reverts the action of markAsMissing.
void	OutlierFlaggingServiceImpl.unmarkAsMissing(Collection<BioAssay> bioAssays)
int	ExpressionDataFileService.writeMexSingleCellExpressionData(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt, ScaleType scaleType, boolean useEnsemblIds, int fetchSize, boolean useCursorFetchIfSupported, boolean forceWrite, Path destDir, boolean autoFlush)
int	ExpressionDataFileService.writeMexSingleCellExpressionData(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt, ScaleType scaleType, boolean useEnsemblIds, OutputStream stream)
int	ExpressionDataFileServiceImpl.writeMexSingleCellExpressionData(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt, ScaleType scaleType, boolean useEnsemblIds, int fetchSize, boolean useCursorFetchIfSupported, boolean forceWrite, Path destDir, boolean autoFlush)
int	ExpressionDataFileServiceImpl.writeMexSingleCellExpressionData(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt, ScaleType scaleType, boolean useEnsemblIds, OutputStream stream)
int	ExpressionDataFileService.writeProcessedExpressionData(ExpressionExperiment ee, List<BioAssay> samples, boolean filtered, ScaleType scaleType, boolean excludeSampleIdentifiers, boolean useBioAssayIds, boolean useRawColumnNames, Writer writer, boolean autoFlush)
int	ExpressionDataFileServiceImpl.writeProcessedExpressionData(ExpressionExperiment ee, List<BioAssay> samples, boolean filtered, ScaleType scaleType, boolean excludeSampleIdentifiers, boolean useBioAssayIds, boolean useRawColumnNames, Writer writer, boolean autoFlush)
int	ExpressionDataFileService.writeRawExpressionData(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt, ScaleType scaleType, boolean excludeSampleIdentifiers, boolean useBioAssayIds, boolean useRawColumnNames, Writer writer, boolean autoFlush)
int	ExpressionDataFileServiceImpl.writeRawExpressionData(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt, ScaleType scaleType, boolean excludeSampleIdentifiers, boolean useBioAssayIds, boolean useRawColumnNames, Writer writer, boolean autoFlush)
int	ExpressionDataFileService.writeTabularSingleCellExpressionData(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt, ScaleType scaleType, boolean useBioAssayIds, boolean useRawColumnNames, int fetchSize, boolean useCursorFetchIfSupported, Writer writer, boolean autoFlush)
int	ExpressionDataFileServiceImpl.writeTabularSingleCellExpressionData(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt, ScaleType scaleType, boolean useBioAssayIds, boolean useRawColumnNames, int fetchSize, boolean useCursorFetchIfSupported, Writer writer, boolean autoFlush)

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

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

Modifier and Type	Method	Description
static double	SingleCellDescriptive.mean(SingleCellExpressionDataVector vector, BioAssay sample)	Calculate the mean of a given assay.
static double	SingleCellDescriptive.sampleStandardDeviation(SingleCellExpressionDataVector vector, BioAssay sample)
static double	SingleCellDescriptive.sampleVariance(SingleCellExpressionDataVector vector, BioAssay sample)	Calculate the variance of a given assay.

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

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, 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)
static List<String>	SingleCellSlicerUtils.sliceCellIds(SingleCellDimension singleCellDimension, List<BioAssay> assays, int[] starts, int[] ends, int numCells)
static Set<CellLevelCharacteristics>	SingleCellSlicerUtils.sliceClcs(SingleCellDimension singleCellDimension, List<BioAssay> assays, int[] starts, int[] ends, int numCells)
static Set<CellTypeAssignment>	SingleCellSlicerUtils.sliceCtas(SingleCellDimension singleCellDimension, List<BioAssay> assays, int[] starts, int[] ends, int numCells)

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

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

Modifier and Type	Method	Description
QuantitationType	SingleCellExpressionExperimentAggregateService.aggregateVectors(ExpressionExperiment ee, QuantitationType qt, List<BioAssay> cellBAs, CellLevelCharacteristics cellLevelCharacteristics, ExperimentalFactor factor, Map<Characteristic,FactorValue> cellTypeMapping, SingleCellAggregationConfig config)	Aggregate preferred single-cell data vectors by the given cell-level characteristics.
QuantitationType	SingleCellExpressionExperimentAggregateServiceImpl.aggregateVectors(ExpressionExperiment ee, QuantitationType qt, List<BioAssay> cellBAs, CellLevelCharacteristics cellLevelCharacteristics, ExperimentalFactor factor, Map<Characteristic,FactorValue> cellType2Factor, SingleCellAggregationConfig config)
QuantitationType	SingleCellExpressionExperimentAggregateService.aggregateVectorsByCellType(ExpressionExperiment ee, List<BioAssay> cellBAs, SingleCellAggregationConfig config)	Aggregate preferred single-cell data vectors by the preferred cell type assignment and the only cell type factor of the experiment.
QuantitationType	SingleCellExpressionExperimentAggregateServiceImpl.aggregateVectorsByCellType(ExpressionExperiment ee, List<BioAssay> cellBAs, SingleCellAggregationConfig config)

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

Fields in ubic.gemma.core.datastructure.matrix with type parameters of type BioAssay

Modifier and Type	Field	Description
protected Map<BioAssay,Integer>	AbstractMultiAssayExpressionDataMatrix.columnAssayMap
protected Map<Integer,Collection<BioAssay>>	AbstractMultiAssayExpressionDataMatrix.columnBioAssayMapByInteger

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

Modifier and Type	Method	Description
BioAssay	AbstractBulkExpressionDataMatrix.getBioAssayForColumn(int index)
BioAssay	AbstractMultiAssayExpressionDataMatrix.getBioAssayForColumn(int index)
BioAssay	BulkExpressionDataMatrix.getBioAssayForColumn(int index)	Obtain an assay corresponding to a given column.
BioAssay	EmptySingleCellExpressionDataMatrix.getBioAssayForColumn(int j)
BioAssay	SingleCellExpressionDataDoubleMatrix.getBioAssayForColumn(int j)
BioAssay	SingleCellExpressionDataIntMatrix.getBioAssayForColumn(int j)
BioAssay	SingleCellExpressionDataMatrix.getBioAssayForColumn(int j)	Obtain a bioassay applicable to a given column.

Methods in ubic.gemma.core.datastructure.matrix that return types with arguments of type BioAssay

Modifier and Type	Method	Description
List<BioAssay>	EmptySingleCellExpressionDataMatrix.getBioAssays()
List<BioAssay>	SingleCellExpressionDataDoubleMatrix.getBioAssays()
List<BioAssay>	SingleCellExpressionDataIntMatrix.getBioAssays()
List<BioAssay>	SingleCellExpressionDataMatrix.getBioAssays()	Obtain the list of bioassays.
Collection<BioAssay>	AbstractMultiAssayExpressionDataMatrix.getBioAssaysForColumn(int index)
Collection<BioAssay>	MultiAssayBulkExpressionDataMatrix.getBioAssaysForColumn(int index)
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 BioAssay

Modifier and Type	Method	Description
T	AbstractBulkExpressionDataMatrix.get(CompositeSequence designElement, BioAssay bioAssay)
T	AbstractMultiAssayExpressionDataMatrix.get(CompositeSequence designElement, BioAssay bioAssay)
T	BulkExpressionDataMatrix.get(CompositeSequence designElement, BioAssay bioAssay)	Access a single value of the matrix.
T[]	AbstractBulkExpressionDataMatrix.getColumn(BioAssay bioAssay)
T[]	AbstractMultiAssayExpressionDataMatrix.getColumn(BioAssay bioAssay)
T[]	BulkExpressionDataMatrix.getColumn(BioAssay bioAssay)	Access a single column of the matrix.
double[]	BulkExpressionDataDoubleMatrix.getColumnAsDoubles(BioAssay bioAssay)
double[]	BulkExpressionDataPrimitiveDoubleMatrix.getColumnAsDoubles(BioAssay bioAssay)	Retrieve the given column without boxing.
double[]	ExpressionDataDoubleMatrix.getColumnAsDoubles(BioAssay bioAssay)
int[]	BulkExpressionDataIntMatrix.getColumnAsInts(BioAssay bioAssay)
int[]	BulkExpressionDataPrimitiveIntMatrix.getColumnAsInts(BioAssay bioAssay)	Retrieve the given column without boxing.
int	AbstractBulkExpressionDataMatrix.getColumnIndex(BioAssay bioAssay)
int	AbstractMultiAssayExpressionDataMatrix.getColumnIndex(BioAssay bioAssay)	Obtain the column index of a given assay.
int	BulkExpressionDataMatrix.getColumnIndex(BioAssay bioAssay)
void	ExpressionDataDoubleMatrix.set(CompositeSequence designElement, BioAssay bioAssay, Double value)	Deprecated.

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

Modifier and Type	Method	Description
static <R> DoubleMatrix<R,BioAssay>	ExpressionDataMatrixColumnSort.orderByExperimentalDesign(DoubleMatrix<R,BioAssay> mat, Collection<ExperimentalFactor> factors, ExperimentalFactor primaryFactor)
protected <R, C, V> void	AbstractMultiAssayExpressionDataMatrix.setMatBioAssayValues(AbstractMatrix<R,C,V> mat, Integer rowIndex, V[] vals, Collection<BioAssay> bioAssays, Iterator<BioAssay> it)
protected <R, C, V> void	AbstractMultiAssayExpressionDataMatrix.setMatBioAssayValues(AbstractMatrix<R,C,V> mat, Integer rowIndex, V[] vals, Collection<BioAssay> bioAssays, Iterator<BioAssay> it)

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

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

Modifier and Type	Method	Description
static String	ExpressionDataWriterUtils.constructAssayName(BioAssay ba, boolean useIds, boolean useRawColumnNames)	Construct a BioAssay column name, unprefixed by the BioMaterial from which it originates.
static String	ExpressionDataWriterUtils.constructCellIdName(BioAssay ba, String cellId, boolean useBioAssayIds, boolean useRawColumnNames)	Construct a BioAssay column name, unprefixed by the BioMaterial from which it originates.
static String	ExpressionDataWriterUtils.constructSampleName(BioMaterial bm, BioAssay ba, boolean useIds, boolean useRawColumnNames)	Construct a sample name in case there is only one BioAssay attached to the corresponding BioMaterial.

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

Modifier and Type	Method	Description
static String	ExpressionDataWriterUtils.constructAssaysName(Collection<BioAssay> bas, boolean useIds, boolean useRawColumnNames, char assayDelimiter)
static String	ExpressionDataWriterUtils.constructSampleName(BioMaterial bioMaterial, Collection<BioAssay> bioAssays, boolean useIds, boolean useRawColumnNames, char assayDelimiter)	Construct a BioAssay column name prefixed by the BioMaterial from which it originates.
void	ExperimentalDesignWriter.write(ExpressionExperiment ee, Collection<BioAssay> bioAssays, boolean writeBaseHeader, Writer writer)	Write the experimental design of the given ExpressionExperiment to the given Writer for a given collection of assays.
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.

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

Methods in ubic.gemma.core.loader.expression that return BioAssay

Modifier and Type	Method	Description
static BioAssay	AffyPowerToolsProbesetSummarize.matchBioAssayToCelFileName(Map<String,BioAssay> bmap, String fileName)

Method parameters in ubic.gemma.core.loader.expression with type arguments of type BioAssay

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.
Set<ExperimentalFactor>	AbstractDelegatingDataLoader.getFactors(Collection<BioAssay> samples, Map<BioMaterial,Set<FactorValue>> factorValueAssignments)
Set<ExperimentalFactor>	DataLoader.getFactors(Collection<BioAssay> samples, Map<BioMaterial,Set<FactorValue>> factorValueAssignments)	Load experimental factors present in the data.
Map<BioMaterial,Set<Characteristic>>	AbstractDelegatingDataLoader.getSamplesCharacteristics(Collection<BioAssay> samples)
Map<BioMaterial,Set<Characteristic>>	DataLoader.getSamplesCharacteristics(Collection<BioAssay> samples)	Load samples characteristics present in the data.
static BioAssay	AffyPowerToolsProbesetSummarize.matchBioAssayToCelFileName(Map<String,BioAssay> bmap, String fileName)

Uses of BioAssay in ubic.gemma.core.loader.expression.arrayDesign

Methods in ubic.gemma.core.loader.expression.arrayDesign that return types with arguments of type BioAssay

Modifier and Type	Method	Description
static Map<BioAssay,String>	AffyChipTypeExtractor.getChipTypes(ExpressionExperiment ee, Collection<File> files)	Extract a string like "Rat230_2" from CEL files.

Uses of BioAssay in ubic.gemma.core.loader.expression.geo.singleCell

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

Modifier and Type	Method	Description
protected Set<BioAssay>	GeoBioAssayMapper.matchAllInternal(Collection<BioAssay> bas, String sampleName)

Methods in ubic.gemma.core.loader.expression.geo.singleCell with parameters of type BioAssay

Modifier and Type	Method	Description
List<String>	GeoBioAssayMapper.getCandidateIdentifiers(BioAssay entity)

Method parameters in ubic.gemma.core.loader.expression.geo.singleCell with type arguments of type BioAssay

Modifier and Type	Method	Description
protected Set<BioAssay>	GeoBioAssayMapper.matchAllInternal(Collection<BioAssay> bas, String sampleName)

Uses of BioAssay in ubic.gemma.core.loader.expression.sequencing

Methods in ubic.gemma.core.loader.expression.sequencing that return types with arguments of type BioAssay

Modifier and Type	Method	Description
Map<BioAssay,SequencingMetadata>	AbstractDelegatingSequencingDataLoader.getSequencingMetadata(Collection<BioAssay> samples)
Map<BioAssay,SequencingMetadata>	SequencingDataLoader.getSequencingMetadata(Collection<BioAssay> samples)	Retrieve various sequencing metadata if counting data is present.
Map<BioAssay,SequencingMetadata>	SequencingMetadataFileDataLoader.getSequencingMetadata(Collection<BioAssay> bioAssays)

Method parameters in ubic.gemma.core.loader.expression.sequencing with type arguments of type BioAssay

Modifier and Type	Method	Description
Map<BioAssay,SequencingMetadata>	AbstractDelegatingSequencingDataLoader.getSequencingMetadata(Collection<BioAssay> samples)
Map<BioAssay,SequencingMetadata>	SequencingDataLoader.getSequencingMetadata(Collection<BioAssay> samples)	Retrieve various sequencing metadata if counting data is present.
Map<BioAssay,SequencingMetadata>	SequencingMetadataFileDataLoader.getSequencingMetadata(Collection<BioAssay> bioAssays)

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

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

Modifier and Type	Method	Description
Map<BioAssay,SequencingMetadata>	AbstractDelegatingSingleCellDataLoader.getSequencingMetadata(SingleCellDimension dimension)
Map<BioAssay,SequencingMetadata>	AnnDataSingleCellDataLoader.getSequencingMetadata(Collection<BioAssay> samples)
Map<BioAssay,SequencingMetadata>	AnnDataSingleCellDataLoader.getSequencingMetadata(SingleCellDimension dimension)
Map<BioAssay,SequencingMetadata>	MexSingleCellDataLoader.getSequencingMetadata(Collection<BioAssay> samples)
Map<BioAssay,SequencingMetadata>	MexSingleCellDataLoader.getSequencingMetadata(SingleCellDimension dimension)
Map<BioAssay,SequencingMetadata>	NullSingleCellDataLoader.getSequencingMetadata(Collection<BioAssay> samples)
Map<BioAssay,SequencingMetadata>	NullSingleCellDataLoader.getSequencingMetadata(SingleCellDimension dimension)
Map<BioAssay,SequencingMetadata>	SequencingMetadataFileSingleCellDataLoader.getSequencingMetadata(Collection<BioAssay> samples)
Map<BioAssay,SequencingMetadata>	SequencingMetadataFileSingleCellDataLoader.getSequencingMetadata(SingleCellDimension dimension)
Map<BioAssay,SequencingMetadata>	SingleCellDataLoader.getSequencingMetadata(SingleCellDimension dimension)
Map<BioAssay,SequencingMetadata>	SingleCellDataLoaderService.loadSequencingMetadata(ExpressionExperiment ee, SingleCellDataLoaderConfig config)	Load sequencing metadata.
Map<BioAssay,SequencingMetadata>	SingleCellDataLoaderServiceImpl.loadSequencingMetadata(ExpressionExperiment ee, SingleCellDataLoaderConfig config)

Method parameters in ubic.gemma.core.loader.expression.singleCell with type arguments of type BioAssay

Modifier and Type	Method	Description
Set<ExperimentalFactor>	AnnDataSingleCellDataLoader.getFactors(Collection<BioAssay> samples, Map<BioMaterial,Set<FactorValue>> factorValueAssignments)
Set<ExperimentalFactor>	MexSingleCellDataLoader.getFactors(Collection<BioAssay> samples, Map<BioMaterial,Set<FactorValue>> factorValueAssignments)	MEX does not provide experimental factors.
Set<ExperimentalFactor>	NullSingleCellDataLoader.getFactors(Collection<BioAssay> samples, Map<BioMaterial,Set<FactorValue>> factorValueAssignments)
Map<BioMaterial,Set<Characteristic>>	AnnDataSingleCellDataLoader.getSamplesCharacteristics(Collection<BioAssay> samples)
Map<BioMaterial,Set<Characteristic>>	MexSingleCellDataLoader.getSamplesCharacteristics(Collection<BioAssay> samples)	MEX does not provide sample characteristics.
Map<BioMaterial,Set<Characteristic>>	NullSingleCellDataLoader.getSamplesCharacteristics(Collection<BioAssay> samples)
Map<BioAssay,SequencingMetadata>	AnnDataSingleCellDataLoader.getSequencingMetadata(Collection<BioAssay> samples)
Map<BioAssay,SequencingMetadata>	MexSingleCellDataLoader.getSequencingMetadata(Collection<BioAssay> samples)
Map<BioAssay,SequencingMetadata>	NullSingleCellDataLoader.getSequencingMetadata(Collection<BioAssay> samples)
Map<BioAssay,SequencingMetadata>	SequencingMetadataFileSingleCellDataLoader.getSequencingMetadata(Collection<BioAssay> samples)
SingleCellDimension	AbstractDelegatingSingleCellDataLoader.getSingleCellDimension(Collection<BioAssay> bioAssays)
SingleCellDimension	AnnDataSingleCellDataLoader.getSingleCellDimension(Collection<BioAssay> bioAssays)
SingleCellDimension	MexSingleCellDataLoader.getSingleCellDimension(Collection<BioAssay> bioAssays)
SingleCellDimension	NullSingleCellDataLoader.getSingleCellDimension(Collection<BioAssay> bioAssays)
SingleCellDimension	SingleCellDataLoader.getSingleCellDimension(Collection<BioAssay> bioAssays)	Load the single-cell dimension present in the data.

Constructor parameters in ubic.gemma.core.loader.expression.singleCell with type arguments of type BioAssay

Modifier	Constructor	Description
	AnnDataSingleCellDataLoaderConfigurer(Path annDataFile, Collection<BioAssay> bioAssays, BioAssayMapper bioAssayMapper)
	MexSingleCellDataLoaderConfigurer(Path mexDir, Collection<BioAssay> bioAssays, BioAssayMapper bioAssayMapper, Path cellRangerPrefix, GeoSeries geoSeries)

Uses of BioAssay in ubic.gemma.core.loader.util.mapper

Methods in ubic.gemma.core.loader.util.mapper that return types with arguments of type BioAssay

Modifier and Type	Method	Description
EntityMapper.StatefulEntityMapper<BioAssay>	AbstractBioAssayMapper.forCandidates(Collection<BioAssay> candidates)
default EntityMapper.StatefulEntityMapper<BioAssay>	BioAssayMapper.forCandidates(BioAssaySet bioAssaySet)
EntityMapper.StatefulEntityMapper<BioAssay>	RenamingBioAssayMapper.forCandidates(Collection<BioAssay> candidates)
Set<BioAssay>	AbstractBioAssayMapper.matchAll(Collection<BioAssay> candidates, String identifier)
Map<String,Set<BioAssay>>	AbstractBioAssayMapper.matchAll(Collection<BioAssay> candidates, Collection<String> identifiers)
Set<BioAssay>	RenamingBioAssayMapper.matchAll(Collection<BioAssay> bioAssays, String sampleName)
protected abstract Set<BioAssay>	AbstractBioAssayMapper.matchAllInternal(Collection<BioAssay> candidates, String identifier)
Set<BioAssay>	SimpleBioAssayMapper.matchAllInternal(Collection<BioAssay> bas, String n)
Optional<BioAssay>	AbstractBioAssayMapper.matchOne(Collection<BioAssay> candidates, String identifier)
Map<String,BioAssay>	AbstractBioAssayMapper.matchOne(Collection<BioAssay> candidates, Collection<String> identifiers)
Optional<BioAssay>	RenamingBioAssayMapper.matchOne(Collection<BioAssay> bioAssays, String sampleName)

Methods in ubic.gemma.core.loader.util.mapper with parameters of type BioAssay

Modifier and Type	Method	Description
List<String>	SimpleBioAssayMapper.getCandidateIdentifiers(BioAssay entity)

Method parameters in ubic.gemma.core.loader.util.mapper with type arguments of type BioAssay

Modifier and Type	Method	Description
boolean	AbstractBioAssayMapper.contains(Collection<BioAssay> candidates, String identifier)
boolean	RenamingBioAssayMapper.contains(Collection<BioAssay> bioAssays, String sampleName)
boolean	AbstractBioAssayMapper.containsAny(Collection<BioAssay> candidates, Collection<String> identifiers)
boolean	RenamingBioAssayMapper.containsAny(Collection<BioAssay> bioAssays, Collection<String> sampleNames)
EntityMapper.StatefulEntityMapper<BioAssay>	AbstractBioAssayMapper.forCandidates(Collection<BioAssay> candidates)
EntityMapper.StatefulEntityMapper<BioAssay>	RenamingBioAssayMapper.forCandidates(Collection<BioAssay> candidates)
static String	EntityMapperUtils.getPossibleIdentifiers(Collection<BioAssay> bioAssays, EntityMapper<BioAssay> mapper)	Render a breakdown of possible BioAssay -> sample identifier associations.
static String	EntityMapperUtils.getPossibleIdentifiers(Collection<BioAssay> bioAssays, EntityMapper<BioAssay> mapper)	Render a breakdown of possible BioAssay -> sample identifier associations.
Set<BioAssay>	AbstractBioAssayMapper.matchAll(Collection<BioAssay> candidates, String identifier)
Map<String,Set<BioAssay>>	AbstractBioAssayMapper.matchAll(Collection<BioAssay> candidates, Collection<String> identifiers)
Set<BioAssay>	RenamingBioAssayMapper.matchAll(Collection<BioAssay> bioAssays, String sampleName)
protected abstract Set<BioAssay>	AbstractBioAssayMapper.matchAllInternal(Collection<BioAssay> candidates, String identifier)
Set<BioAssay>	SimpleBioAssayMapper.matchAllInternal(Collection<BioAssay> bas, String n)
Optional<BioAssay>	AbstractBioAssayMapper.matchOne(Collection<BioAssay> candidates, String identifier)
Map<String,BioAssay>	AbstractBioAssayMapper.matchOne(Collection<BioAssay> candidates, Collection<String> identifiers)
Optional<BioAssay>	RenamingBioAssayMapper.matchOne(Collection<BioAssay> bioAssays, String sampleName)
protected <T> boolean	AbstractBioAssayMapper.matchWithFunction(Collection<BioAssay> bas, Function<BioAssay,T> extractor, BiFunction<T,String,Boolean> func, String sampleName, Collection<BioAssay> results)
protected <T> boolean	AbstractBioAssayMapper.matchWithFunction(Collection<BioAssay> bas, Function<BioAssay,T> extractor, BiFunction<T,String,Boolean> func, String sampleName, Collection<BioAssay> results)

Constructor parameters in ubic.gemma.core.loader.util.mapper with type arguments of type BioAssay

Modifier	Constructor	Description
	CellIdOverlapBioAssayMapper(Map<BioAssay,Set<String>> bioAssayToCellIds, Map<String,Set<String>> sampleNameToCellIds)

Uses of BioAssay in ubic.gemma.core.visualization

Methods in ubic.gemma.core.visualization that return types with arguments of type BioAssay

Modifier and Type	Method	Description
List<BioAssay>	ExpressionDataHeatmap.getAssays()
Map<BioAssay,Long>	SingleCellSparsityHeatmap.getDesignElementsPerSample()
List<BioAssay>	SingleCellSparsityHeatmap.getSamples()

Method parameters in ubic.gemma.core.visualization with type arguments of type BioAssay

Modifier and Type	Method	Description
void	SingleCellDataBoxplot.setBioAssays(List<BioAssay> bioAssays)

Constructor parameters in ubic.gemma.core.visualization with type arguments of type BioAssay

Modifier	Constructor	Description
	SingleCellSparsityHeatmap(ExpressionExperiment expressionExperiment, SingleCellDimension singleCellDimension, BioAssayDimension dimension, Collection<ExpressionExperimentSubSet> subSets, Map<BioAssay,Long> designElementsPerSample, SingleCellSparsityHeatmap.SingleCellHeatmapType type)

Uses of BioAssay in ubic.gemma.core.visualization.cellbrowser

Methods in ubic.gemma.core.visualization.cellbrowser with parameters of type BioAssay

Modifier and Type	Method	Description
static String	CellBrowserUtils.constructCellId(BioAssay bioAssay, String cellId, boolean useBioAssayIds, boolean useRawColumnNames)	Construct a cell ID for the Cell Browser.
void	CellBrowserMetadataWriter.writeCell(BioAssay bioAssay, String cellId, int cellIndex, List<ExperimentalFactor> factors, Map<ExperimentalFactor,Map<BioMaterial,FactorValue>> factorValueMap, SortedMap<Category,Map<BioAssay,Characteristic>> bioAssayCharacteristics, SortedMap<Category,Map<BioMaterial,Characteristic>> sampleCharacteristics, List<CellLevelCharacteristics> clcs, Writer writer)

Method parameters in ubic.gemma.core.visualization.cellbrowser with type arguments of type BioAssay

Modifier and Type	Method	Description
void	CellBrowserMetadataWriter.writeCell(BioAssay bioAssay, String cellId, int cellIndex, List<ExperimentalFactor> factors, Map<ExperimentalFactor,Map<BioMaterial,FactorValue>> factorValueMap, SortedMap<Category,Map<BioAssay,Characteristic>> bioAssayCharacteristics, SortedMap<Category,Map<BioMaterial,Characteristic>> sampleCharacteristics, List<CellLevelCharacteristics> clcs, Writer writer)

Uses of BioAssay in ubic.gemma.model.expression.bioAssay

Methods in ubic.gemma.model.expression.bioAssay that return BioAssay

Modifier and Type	Method	Description
static BioAssay	BioAssay.Factory.newInstance()
static BioAssay	BioAssay.Factory.newInstance(String name)
static BioAssay	BioAssay.Factory.newInstance(String name, ArrayDesign arrayDesignUsed, BioMaterial sampleUsed)

Methods in ubic.gemma.model.expression.bioAssay that return types with arguments of type BioAssay

Modifier and Type	Method	Description
static Map<BioAssay,BioAssay>	BioAssayUtils.createBioAssayToSourceBioAssayMap(BioAssaySet sourceAssaySet, Collection<BioAssay> bas)	Create a mapping between assays and their source assays from a given BioAssaySet.
static Map<BioAssay,BioAssay>	BioAssayUtils.createBioAssayToSourceBioAssayMap(BioAssaySet sourceAssaySet, Collection<BioAssay> bas)	Create a mapping between assays and their source assays from a given BioAssaySet.
static Map<Category,Map<BioAssay,Collection<Characteristic>>>	BioAssayUtils.createCharacteristicMap(Collection<BioAssay> assays)	Create a mapping of biomaterial to characteristics for each category.

Method parameters in ubic.gemma.model.expression.bioAssay with type arguments of type BioAssay

Modifier and Type	Method	Description
static Map<BioAssay,BioAssay>	BioAssayUtils.createBioAssayToSourceBioAssayMap(BioAssaySet sourceAssaySet, Collection<BioAssay> bas)	Create a mapping between assays and their source assays from a given BioAssaySet.
static Map<Category,Map<BioAssay,Collection<Characteristic>>>	BioAssayUtils.createCharacteristicMap(Collection<BioAssay> assays)	Create a mapping of biomaterial to characteristics for each category.

Constructors in ubic.gemma.model.expression.bioAssay with parameters of type BioAssay

Modifier	Constructor	Description
	BioAssayValueObject(BioAssay bioAssay)
	BioAssayValueObject(BioAssay bioAssay, boolean basic)
	BioAssayValueObject(BioAssay bioAssay, boolean basic, boolean predictedOutlier)
	BioAssayValueObject(BioAssay bioAssay, Map<ArrayDesign,ArrayDesignValueObject> ad2vo, BioAssay sourceBioAssay, boolean basic, boolean allFactorValues)

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

Methods in ubic.gemma.model.expression.bioAssayData that return BioAssay

Modifier and Type	Method	Description
BioAssay	SingleCellDimension.getBioAssay(int cellIndex)	Obtain the BioAssay for a given cell position.

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

Modifier and Type	Method	Description
static Map<BioAssay,Map<String,Integer>>	SingleCellDimensionUtils.createIndex(SingleCellDimension singleCellDimension)	Create an index of bioassays to their cell IDs and their position in the bioassays.
static Map<String,Map<BioAssay,Integer>>	SingleCellDimensionUtils.createReverseIndex(SingleCellDimension singleCellDimension)	Create a reverse index of cell IDs to their corresponding position in bioassays.
List<BioAssay>	BioAssayDimension.getBioAssays()
List<BioAssay>	SingleCellDimension.getBioAssays()	List of BioAssays applicable to the cells.

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

Modifier and Type	Method	Description
static double[]	SingleCellExpressionDataVectorUtils.getSampleDataAsDoubles(SingleCellExpressionDataVector vector, BioAssay 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, BioAssay sample)
static int	SingleCellExpressionDataVectorUtils.getSampleStart(SingleCellExpressionDataVector vector, BioAssay sample, int after)

Method parameters in ubic.gemma.model.expression.bioAssayData with type arguments of type BioAssay

Modifier and Type	Method	Description
static BioAssayDimension	BioAssayDimension.Factory.newInstance(List<BioAssay> bioAssays)
void	BioAssayDimension.setBioAssays(List<BioAssay> bioAssays)
void	SingleCellDimension.setBioAssays(List<BioAssay> bioAssays)	List of BioAssays applicable to the cells.

Uses of BioAssay in ubic.gemma.model.expression.biomaterial

Methods in ubic.gemma.model.expression.biomaterial that return types with arguments of type BioAssay

Modifier and Type	Method	Description
Set<BioAssay>	BioMaterial.getAllBioAssaysUsedIn()	Obtain all the assays used in the hierarchy of biomaterials via BioMaterial.getSourceBioMaterial().
Set<BioAssay>	BioMaterial.getBioAssaysUsedIn()

Method parameters in ubic.gemma.model.expression.biomaterial with type arguments of type BioAssay

Modifier and Type	Method	Description
void	BioMaterial.setBioAssaysUsedIn(Set<BioAssay> bioAssaysUsedIn)

Constructors in ubic.gemma.model.expression.biomaterial with parameters of type BioAssay

Modifier	Constructor	Description
	BioMaterialValueObject(BioMaterial bm, BioAssay ba)

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

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

Modifier and Type	Method	Description
Set<BioAssay>	BioAssaySet.getBioAssays()
Set<BioAssay>	ExpressionExperiment.getBioAssays()

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

Modifier and Type	Method	Description
void	BioAssaySet.setBioAssays(Set<BioAssay> bioAssays)

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

Methods in ubic.gemma.persistence.service.analysis.expression.sampleCoexpression that return types with arguments of type BioAssay

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>	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>	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>	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>	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>	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>	SampleCoexpressionAnalysisServiceImpl.loadFullMatrix(ExpressionExperiment ee)
DoubleMatrix<BioAssay,BioAssay>	SampleCoexpressionAnalysisService.loadRegressedMatrix(ExpressionExperiment ee)	Load the regressed coexpression matrix for the given experiment.
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>	SampleCoexpressionAnalysisServiceImpl.loadRegressedMatrix(ExpressionExperiment ee)
DoubleMatrix<BioAssay,BioAssay>	SampleCoexpressionAnalysisService.retrieveExisting(ExpressionExperiment ee)
DoubleMatrix<BioAssay,BioAssay>	SampleCoexpressionAnalysisService.retrieveExisting(ExpressionExperiment ee)
DoubleMatrix<BioAssay,BioAssay>	SampleCoexpressionAnalysisServiceImpl.retrieveExisting(ExpressionExperiment ee)
DoubleMatrix<BioAssay,BioAssay>	SampleCoexpressionAnalysisServiceImpl.retrieveExisting(ExpressionExperiment ee)

Uses of BioAssay in ubic.gemma.persistence.service.expression.arrayDesign

Methods in ubic.gemma.persistence.service.expression.arrayDesign that return types with arguments of type BioAssay

Modifier and Type	Method	Description
Collection<BioAssay>	ArrayDesignDao.getAllAssociatedBioAssays(ArrayDesign arrayDesign)
Collection<BioAssay>	ArrayDesignDaoImpl.getAllAssociatedBioAssays(ArrayDesign arrayDesign)
Collection<BioAssay>	ArrayDesignService.getAllAssociatedBioAssays(ArrayDesign arrayDesign)
Collection<BioAssay>	ArrayDesignServiceImpl.getAllAssociatedBioAssays(ArrayDesign arrayDesign)

Uses of BioAssay in ubic.gemma.persistence.service.expression.bioAssay

Methods in ubic.gemma.persistence.service.expression.bioAssay that return BioAssay

Modifier and Type	Method	Description
BioAssay	BioAssayService.create(BioAssay bioAssay)
BioAssay	BioAssayDaoImpl.find(BioAssay bioAssay)
BioAssay	BioAssayDao.findByShortName(String shortName)
BioAssay	BioAssayDaoImpl.findByShortName(String shortName)
BioAssay	BioAssayService.findByShortName(String shortName)
BioAssay	BioAssayServiceImpl.findByShortName(String shortName)
BioAssay	BioAssayService.findOrCreate(BioAssay bioAssay)
BioAssay	BioAssayService.load(Long id)
BioAssay	BioAssayService.thaw(BioAssay bioAssay)
BioAssay	BioAssayServiceImpl.thaw(BioAssay ba)

Methods in ubic.gemma.persistence.service.expression.bioAssay that return types with arguments of type BioAssay

Modifier and Type	Method	Description
Collection<BioAssay>	BioAssayDao.findByAccession(String accession)
Collection<BioAssay>	BioAssayDaoImpl.findByAccession(String accession)
Collection<BioAssay>	BioAssayService.findByAccession(String accession)
Collection<BioAssay>	BioAssayServiceImpl.findByAccession(String accession)
Collection<BioAssay>	BioAssayService.findSiblings(BioAssay bioAssay)
Collection<BioAssay>	BioAssayServiceImpl.findSiblings(BioAssay bioAssay)
Collection<BioAssay>	BioAssayService.findSubBioAssays(BioAssay bioAssay, boolean direct)
Collection<BioAssay>	BioAssayServiceImpl.findSubBioAssays(BioAssay bioAssay, boolean direct)
Collection<BioAssay>	BioAssayService.load(Collection<Long> ids)
Collection<BioAssay>	BioAssayService.loadAll()
Collection<BioAssay>	BioAssayService.thaw(Collection<BioAssay> bioAssays)
Collection<BioAssay>	BioAssayServiceImpl.thaw(Collection<BioAssay> bioAssays)

Methods in ubic.gemma.persistence.service.expression.bioAssay with parameters of type BioAssay

Modifier and Type	Method	Description
void	BioAssayService.addBioMaterialAssociation(BioAssay bioAssay, BioMaterial bioMaterial)	Associates a bioMaterial with a specified bioAssay.
void	BioAssayServiceImpl.addBioMaterialAssociation(BioAssay bioAssay, BioMaterial bioMaterial)
BioAssay	BioAssayService.create(BioAssay bioAssay)
protected BioAssayValueObject	BioAssayDaoImpl.doLoadValueObject(BioAssay entity)
BioAssay	BioAssayDaoImpl.find(BioAssay bioAssay)
Collection<BioAssayDimension>	BioAssayDao.findBioAssayDimensions(BioAssay bioAssay)
Collection<BioAssayDimension>	BioAssayDaoImpl.findBioAssayDimensions(BioAssay bioAssay)
Collection<BioAssayDimension>	BioAssayService.findBioAssayDimensions(BioAssay bioAssay)	Locate all BioAssayDimensions in which the selected BioAssay occurs
Collection<BioAssayDimension>	BioAssayServiceImpl.findBioAssayDimensions(BioAssay bioAssay)
BioAssay	BioAssayService.findOrCreate(BioAssay bioAssay)
Collection<BioAssay>	BioAssayService.findSiblings(BioAssay bioAssay)
Collection<BioAssay>	BioAssayServiceImpl.findSiblings(BioAssay bioAssay)
Collection<BioAssay>	BioAssayService.findSubBioAssays(BioAssay bioAssay, boolean direct)
Collection<BioAssay>	BioAssayServiceImpl.findSubBioAssays(BioAssay bioAssay, boolean direct)
Collection<BioAssaySet>	BioAssayDao.getBioAssaySets(BioAssay bioAssay)
Collection<BioAssaySet>	BioAssayDaoImpl.getBioAssaySets(BioAssay bioAssay)
Collection<BioAssaySet>	BioAssayService.getBioAssaySets(BioAssay bioAssay)	Obtain all the BioAssaySet that contain the given BioAssay.
Collection<BioAssaySet>	BioAssayServiceImpl.getBioAssaySets(BioAssay bioAssay)
void	BioAssayService.remove(BioAssay bioAssay)
void	BioAssayService.removeBioMaterialAssociation(BioAssay bioAssay, BioMaterial bioMaterial)	Removes the association between a specific bioMaterial and a bioAssay.
void	BioAssayServiceImpl.removeBioMaterialAssociation(BioAssay bioAssay, BioMaterial bioMaterial)
BioAssay	BioAssayService.thaw(BioAssay bioAssay)
BioAssay	BioAssayServiceImpl.thaw(BioAssay ba)
void	BioAssayService.update(BioAssay bioAssay)

Method parameters in ubic.gemma.persistence.service.expression.bioAssay with type arguments of type BioAssay

Modifier and Type	Method	Description
List<BioAssayValueObject>	BioAssayDao.loadValueObjects(Collection<BioAssay> entities, Map<ArrayDesign,ArrayDesignValueObject> ad2vo, Map<BioAssay,BioAssay> assay2sourceAssayMap, boolean basic, boolean allFactorValues)
List<BioAssayValueObject>	BioAssayDaoImpl.loadValueObjects(Collection<BioAssay> entities, Map<ArrayDesign,ArrayDesignValueObject> ad2vo, Map<BioAssay,BioAssay> assay2sourceAssayMap, boolean basic, boolean allFactorValues)
List<BioAssayValueObject>	BioAssayService.loadValueObjects(Collection<BioAssay> entities, Map<BioAssay,BioAssay> assay2sourceAssayMap, boolean basic, boolean allFactorValues)
List<BioAssayValueObject>	BioAssayService.loadValueObjects(Collection<BioAssay> entities, Map<BioAssay,BioAssay> assay2sourceAssayMap, boolean basic, boolean allFactorValues)
List<BioAssayValueObject>	BioAssayService.loadValueObjects(Collection<BioAssay> entities, Map<BioAssay,BioAssay> assay2sourceAssayMap, boolean basic, boolean allFactorValues)
List<BioAssayValueObject>	BioAssayServiceImpl.loadValueObjects(Collection<BioAssay> entities, Map<BioAssay,BioAssay> assay2sourceAssayMap, boolean basic, boolean allFactorValues)
List<BioAssayValueObject>	BioAssayServiceImpl.loadValueObjects(Collection<BioAssay> entities, Map<BioAssay,BioAssay> assay2sourceAssayMap, boolean basic, boolean allFactorValues)
List<BioAssayValueObject>	BioAssayServiceImpl.loadValueObjects(Collection<BioAssay> entities, Map<BioAssay,BioAssay> assay2sourceAssayMap, boolean basic, boolean allFactorValues)
Collection<BioAssay>	BioAssayService.thaw(Collection<BioAssay> bioAssays)
Collection<BioAssay>	BioAssayServiceImpl.thaw(Collection<BioAssay> bioAssays)

Uses of BioAssay in ubic.gemma.persistence.service.expression.bioAssayData

Method parameters in ubic.gemma.persistence.service.expression.bioAssayData with type arguments of type BioAssay

Modifier and Type	Method	Description
Collection<BioAssayDimension>	BioAssayDimensionDao.findByBioAssaysContainingAll(Collection<BioAssay> bioAssays)	Find all the dimensions that contains all the given assays.
Collection<BioAssayDimension>	BioAssayDimensionDaoImpl.findByBioAssaysContainingAll(Collection<BioAssay> bioAssays)
Collection<BioAssayDimension>	BioAssayDimensionService.findByBioAssaysContainingAll(Collection<BioAssay> bioAssays)
Collection<BioAssayDimension>	BioAssayDimensionServiceImpl.findByBioAssaysContainingAll(Collection<BioAssay> bioAssays)

Uses of BioAssay in ubic.gemma.persistence.service.expression.biomaterial

Methods in ubic.gemma.persistence.service.expression.biomaterial that return types with arguments of type BioAssay

Modifier and Type	Method	Description
Map<BioMaterial,Map<BioAssay,ExpressionExperiment>>	BioMaterialDao.getExpressionExperiments(BioMaterial bm)	Obtain all the experiments a biomaterial is used in from its hierarchy.
Map<BioMaterial,Map<BioAssay,ExpressionExperiment>>	BioMaterialDaoImpl.getExpressionExperiments(BioMaterial bm)
Map<BioMaterial,Map<BioAssay,ExpressionExperiment>>	BioMaterialService.getExpressionExperiments(BioMaterial bm)
Map<BioMaterial,Map<BioAssay,ExpressionExperiment>>	BioMaterialServiceImpl.getExpressionExperiments(BioMaterial bm)

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

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

Modifier and Type	Method	Description
Map<BioAssay,Long>	ExpressionExperimentDao.getNumberOfDesignElementsPerSample(ExpressionExperiment expressionExperiment)
Map<BioAssay,Long>	ExpressionExperimentDaoImpl.getNumberOfDesignElementsPerSample(ExpressionExperiment expressionExperiment)
Map<BioAssay,Long>	ExpressionExperimentService.getNumberOfDesignElementsPerSample(ExpressionExperiment expressionExperiment)	Obtain the number of design elements for the platform of each bioassay in the given experiment.
Map<BioAssay,Long>	ExpressionExperimentServiceImpl.getNumberOfDesignElementsPerSample(ExpressionExperiment expressionExperiment)
Map<BioAssay,Long>	ExpressionExperimentDao.getNumberOfNonZeroesBySample(ExpressionExperiment ee, QuantitationType qt, int fetchSize, boolean useCursorFetchIfSupported)	Obtain the number of non-zeroes by sample.
Map<BioAssay,Long>	ExpressionExperimentDaoImpl.getNumberOfNonZeroesBySample(ExpressionExperiment ee, QuantitationType qt, int fetchSize, boolean useCursorFetchIfSupported)
Map<BioAssay,Long>	SingleCellExpressionExperimentService.getNumberOfNonZeroesBySample(ExpressionExperiment ee, QuantitationType qt, int fetchSize, boolean useCursorFetchIfSupported)
Map<BioAssay,Long>	SingleCellExpressionExperimentServiceImpl.getNumberOfNonZeroesBySample(ExpressionExperiment ee, QuantitationType qt, int fetchSize, boolean useCursorFetchIfSupported)

Methods in ubic.gemma.persistence.service.expression.experiment with parameters of type BioAssay

Modifier and Type	Method	Description
ExpressionExperiment	ExpressionExperimentDao.findByBioAssay(BioAssay ba)
ExpressionExperiment	ExpressionExperimentDaoImpl.findByBioAssay(BioAssay ba)
ExpressionExperiment	ExpressionExperimentService.findByBioAssay(BioAssay ba)
ExpressionExperiment	ExpressionExperimentServiceImpl.findByBioAssay(BioAssay ba)

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

Modifier and Type	Method	Description
Collection<ExpressionExperimentSubSet>	ExpressionExperimentSubSetDao.findByBioAssayIn(Collection<BioAssay> bioAssays)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentSubSetDaoImpl.findByBioAssayIn(Collection<BioAssay> bioAssays)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentSubSetService.findByBioAssayIn(Collection<BioAssay> bioAssays)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentSubSetServiceImpl.findByBioAssayIn(Collection<BioAssay> bioAssays)
Collection<ProcessedExpressionDataVector>	ExpressionExperimentDao.getProcessedDataVectors(ExpressionExperiment ee, List<BioAssay> assays)	Retrieve a slice of processed vectors for an experiment.
Collection<ProcessedExpressionDataVector>	ExpressionExperimentDaoImpl.getProcessedDataVectors(ExpressionExperiment ee, List<BioAssay> assays)
Optional<Collection<ProcessedExpressionDataVector>>	ExpressionExperimentService.getProcessedDataVectors(ExpressionExperiment ee, List<BioAssay> assays)
Optional<Collection<ProcessedExpressionDataVector>>	ExpressionExperimentServiceImpl.getProcessedDataVectors(ExpressionExperiment ee, List<BioAssay> assays)
Collection<RawExpressionDataVector>	ExpressionExperimentDao.getRawDataVectors(ExpressionExperiment ee, List<BioAssay> assays, QuantitationType qt)	Obtain a slice of the raw vectors for a given experiment and QT.
Collection<RawExpressionDataVector>	ExpressionExperimentDaoImpl.getRawDataVectors(ExpressionExperiment ee, List<BioAssay> assays, QuantitationType qt)
Collection<RawExpressionDataVector>	ExpressionExperimentService.getRawDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt)
Collection<RawExpressionDataVector>	ExpressionExperimentServiceImpl.getRawDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt)
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>	SingleCellExpressionExperimentServiceImpl.getSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType)
Collection<SingleCellExpressionDataVector>	SingleCellExpressionExperimentServiceImpl.getSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)
SingleCellExpressionDataMatrix<?>	SingleCellExpressionExperimentService.getSingleCellExpressionDataMatrix(ExpressionExperiment expressionExperiment, List<BioAssay> samples, QuantitationType quantitationType)	Obtain a single-cell expression data matrix for the given quantitation type.
SingleCellExpressionDataMatrix<?>	SingleCellExpressionExperimentServiceImpl.getSingleCellExpressionDataMatrix(ExpressionExperiment expressionExperiment, List<BioAssay> samples, QuantitationType quantitationType)
Stream<SingleCellExpressionDataVector>	SingleCellExpressionExperimentService.streamSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType, int fetchSize, boolean useCursorFetchIfSupported, boolean createNewSession)
Stream<SingleCellExpressionDataVector>	SingleCellExpressionExperimentService.streamSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType, int fetchSize, boolean useCursorFetchIfSupported, boolean createNewSession, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)
Stream<SingleCellExpressionDataVector>	SingleCellExpressionExperimentServiceImpl.streamSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType, int fetchSize, boolean useCursorFetchIfSupported, boolean createNewSession)
Stream<SingleCellExpressionDataVector>	SingleCellExpressionExperimentServiceImpl.streamSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType, int fetchSize, boolean useCursorFetchIfSupported, boolean createNewSession, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)

Uses of BioAssay in ubic.gemma.persistence.util

Methods in ubic.gemma.persistence.util with parameters of type BioAssay

Modifier and Type	Method	Description
static void	BusinessKey.addRestrictions(Criteria queryObject, BioAssay bioAssay)
static Criteria	BusinessKey.createQueryObject(Session session, BioAssay bioAssay)
static void	Thaws.thawBioAssay(BioAssay ba)	Thaw the given BioAssay.

Method parameters in ubic.gemma.persistence.util with type arguments of type BioAssay

Modifier and Type	Method	Description
EntityUrlBuilder.ExpressionExperimentWebUrl	EntityUrlBuilder.ExpressionExperimentWebUrl.showSingleCellExpressionData(QuantitationType quantitationType, CompositeSequence designElement, List<BioAssay> assays, CellLevelCharacteristics cellLevelCharacteristics, Characteristic focusedCharacteristic)