Package ubic.gemma.core.loader.expression.singleCell

Class SingleCellDataLoaderServiceImpl

java.lang.Object

ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderServiceImpl

All Implemented Interfaces:

SingleCellDataLoaderService

@Service
public class SingleCellDataLoaderServiceImpl
extends Object
implements SingleCellDataLoaderService

Constructor Summary

Constructors

Constructor	Description
SingleCellDataLoaderServiceImpl()

Method Summary

Modifier and Type	Method	Description
Path	getSeuratDiskFile(ExpressionExperiment ee)
QuantitationType	load(ExpressionExperiment ee, ArrayDesign platform, SingleCellDataLoaderConfig config)	Load single-cell data, the data type is automatically detected.
QuantitationType	load(ExpressionExperiment ee, ArrayDesign platform, SingleCellDataType dataType, SingleCellDataLoaderConfig config)	Load a specific single-cell data type.
Collection<CellTypeAssignment>	loadCellTypeAssignments(ExpressionExperiment ee, SingleCellDataLoaderConfig config)	Load the cell type assignments, the data type is automatically detected.
Collection<CellTypeAssignment>	loadCellTypeAssignments(ExpressionExperiment ee, SingleCellDataType dataType, SingleCellDataLoaderConfig config)	Load the cell type assignments.
Collection<CellLevelCharacteristics>	loadOtherCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDataLoaderConfig config)	Load other cell-level characteristics (i.e.
Collection<CellLevelCharacteristics>	loadOtherCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDataType dataType, SingleCellDataLoaderConfig config)	Load other cell-level characteristics (i.e.
Map<BioAssay,SequencingMetadata>	loadSequencingMetadata(ExpressionExperiment ee, SingleCellDataLoaderConfig config)	Load sequencing metadata.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

SingleCellDataLoaderServiceImpl

public SingleCellDataLoaderServiceImpl()

Method Details

load

@Transactional
public QuantitationType load(ExpressionExperiment ee,
 ArrayDesign platform,
 SingleCellDataLoaderConfig config)

Description copied from interface: SingleCellDataLoaderService

Load single-cell data, the data type is automatically detected.

Specified by:

load in interface SingleCellDataLoaderService

See Also:

• SingleCellDataLoaderService.load(ExpressionExperiment, ArrayDesign, SingleCellDataType, SingleCellDataLoaderConfig)

load

@Transactional
public QuantitationType load(ExpressionExperiment ee,
 ArrayDesign platform,
 SingleCellDataType dataType,
 SingleCellDataLoaderConfig config)

Description copied from interface: SingleCellDataLoaderService

Load a specific single-cell data type.

Specified by:

load in interface SingleCellDataLoaderService

Parameters:

ee - experiment to load data into

platform - platform to use to associate data vectors to

dataType - data type to detect

config - a configuration

loadSequencingMetadata

@Transactional
public Map<BioAssay,SequencingMetadata> loadSequencingMetadata(ExpressionExperiment ee,
 SingleCellDataLoaderConfig config)

Description copied from interface: SingleCellDataLoaderService

Load sequencing metadata.

Specified by:

loadSequencingMetadata in interface SingleCellDataLoaderService

loadCellTypeAssignments

@Transactional
public Collection<CellTypeAssignment> loadCellTypeAssignments(ExpressionExperiment ee,
 SingleCellDataLoaderConfig config)

Description copied from interface: SingleCellDataLoaderService

Load the cell type assignments, the data type is automatically detected.

Specified by:

loadCellTypeAssignments in interface SingleCellDataLoaderService

See Also:

• SingleCellDataLoaderService.loadOtherCellLevelCharacteristics(ExpressionExperiment, SingleCellDataType, SingleCellDataLoaderConfig)

loadCellTypeAssignments

@Transactional
public Collection<CellTypeAssignment> loadCellTypeAssignments(ExpressionExperiment ee,
 SingleCellDataType dataType,
 SingleCellDataLoaderConfig config)

Description copied from interface: SingleCellDataLoaderService

Load the cell type assignments.

The dataset must already have a set of preferred single-cell vectors loaded or one identified by DataLoaderConfig.getQuantitationTypeName().

Specified by:

loadCellTypeAssignments in interface SingleCellDataLoaderService

loadOtherCellLevelCharacteristics

@Transactional
public Collection<CellLevelCharacteristics> loadOtherCellLevelCharacteristics(ExpressionExperiment ee,
 SingleCellDataLoaderConfig config)

Description copied from interface: SingleCellDataLoaderService

Load other cell-level characteristics (i.e. anything that is not a cell type assignment), the data type is automatically detected.

Specified by:

loadOtherCellLevelCharacteristics in interface SingleCellDataLoaderService

See Also:

• SingleCellDataLoaderService.loadOtherCellLevelCharacteristics(ExpressionExperiment, SingleCellDataType, SingleCellDataLoaderConfig)

loadOtherCellLevelCharacteristics

@Transactional
public Collection<CellLevelCharacteristics> loadOtherCellLevelCharacteristics(ExpressionExperiment ee,
 SingleCellDataType dataType,
 SingleCellDataLoaderConfig config)

Description copied from interface: SingleCellDataLoaderService

Load other cell-level characteristics (i.e. anything that is not a cell type assignment).

The dataset must already have a set of preferred single-cell vectors loaded or one identified by DataLoaderConfig.getQuantitationTypeName().

Specified by:

loadOtherCellLevelCharacteristics in interface SingleCellDataLoaderService

getSeuratDiskFile

public Path getSeuratDiskFile(ExpressionExperiment ee)