Uses of Class
ubic.gemma.core.loader.expression.sequencing.SequencingMetadata

Packages that use SequencingMetadata

Package	Description
ubic.gemma.core.loader.expression	This package contains interfaces and classes for loading expression data.
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.

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

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

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.

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

Methods in ubic.gemma.core.loader.expression.sequencing that return SequencingMetadata

Modifier and Type	Method	Description
SequencingMetadata	SequencingMetadata.SequencingMetadataBuilder.build()
SequencingMetadata	SequencingDataLoaderConfig.getDefaultSequencingMetadata()	Default sequencing metadata to use.

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

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)

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

Modifier and Type	Method	Description
B	SequencingDataLoaderConfig.SequencingDataLoaderConfigBuilder.defaultSequencingMetadata(SequencingMetadata defaultSequencingMetadata)	Default sequencing metadata to use.

Constructors in ubic.gemma.core.loader.expression.sequencing with parameters of type SequencingMetadata

Modifier	Constructor	Description
	SequencingMetadataFileDataLoader(SequencingDataLoader delegate, Path sequencingMetadataFile, SequencingMetadata defaultMetadata, BioAssayMapper bioAssayMapper)

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

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

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)

Constructors in ubic.gemma.core.loader.expression.singleCell with parameters of type SequencingMetadata

Modifier	Constructor	Description
	SequencingMetadataFileSingleCellDataLoader(SingleCellDataLoader delegate, Path sequencingMetadataFile, SequencingMetadata defaultMetadata, BioAssayMapper bioAssayMapper)