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

Interface SingleCellDataLoaderService

All Known Implementing Classes:

SingleCellDataLoaderServiceImpl

public interface SingleCellDataLoaderService

High-level service for loading single-cell data.

Author:

poirigui

Method Summary

Modifier and Type	Method	Description
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. anything that is not a cell type assignment), the data type is automatically detected.
Collection<CellLevelCharacteristics>	loadOtherCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDataType dataType, SingleCellDataLoaderConfig config)	Load other cell-level characteristics (i.e. anything that is not a cell type assignment).
Map<BioAssay,SequencingMetadata>	loadSequencingMetadata(ExpressionExperiment ee, SingleCellDataLoaderConfig config)	Load sequencing metadata.

Method Detail

load

QuantitationType load(ExpressionExperiment ee,
                      ArrayDesign platform,
                      SingleCellDataLoaderConfig config)

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

See Also:

load(ExpressionExperiment, ArrayDesign, SingleCellDataType, SingleCellDataLoaderConfig)

load

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

Load a specific single-cell data type.

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

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

Load sequencing metadata.

loadCellTypeAssignments

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

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

See Also:

loadOtherCellLevelCharacteristics(ExpressionExperiment, SingleCellDataType, SingleCellDataLoaderConfig)

loadCellTypeAssignments

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

Load the cell type assignments.

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

loadOtherCellLevelCharacteristics

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

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

See Also:

loadOtherCellLevelCharacteristics(ExpressionExperiment, SingleCellDataType, SingleCellDataLoaderConfig)

loadOtherCellLevelCharacteristics

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

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 SingleCellDataLoaderConfig#getQuantitationTypeName().