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

Interface SingleCellDataLoader

All Superinterfaces:

AutoCloseable, Closeable, DataLoader, SequencingDataLoader

All Known Implementing Classes:

AbstractDelegatingSingleCellDataLoader, AnnDataSingleCellDataLoader, GenericMetadataSingleCellDataLoader, MexSingleCellDataLoader, NullSingleCellDataLoader, SequencingMetadataFileSingleCellDataLoader

public interface SingleCellDataLoader
extends DataLoader, SequencingDataLoader

Common interface for all single-cell data loaders.

Author:

poirigui

Method Summary

Modifier and Type	Method	Description
Set<CellTypeAssignment>	getCellTypeAssignments(SingleCellDimension dimension)	Load single-cell type assignments present in the data.
Set<CellLevelCharacteristics>	getOtherCellLevelCharacteristics(SingleCellDimension dimension)	Load cell-level characteristics that are not cell type assignments present in the data.
Map<BioAssay,SequencingMetadata>	getSequencingMetadata(SingleCellDimension dimension)
SingleCellDimension	getSingleCellDimension(Collection<BioAssay> bioAssays)	Load the single-cell dimension present in the data.
Stream<SingleCellExpressionDataVector>	loadVectors(Collection<CompositeSequence> designElements, SingleCellDimension dimension, QuantitationType quantitationType)	Produces a stream of single-cell expression data vectors for the given QuantitationType.

Methods inherited from interface ubic.gemma.core.loader.expression.DataLoader

close, getFactors, getGenes, getQuantitationTypes, getSampleNames, getSamplesCharacteristics, setBioAssayToSampleNameMapper, setDesignElementToGeneMapper, setIgnoreUnmatchedDesignElements, setIgnoreUnmatchedSamples

Methods inherited from interface ubic.gemma.core.loader.expression.sequencing.SequencingDataLoader

getSequencingMetadata

Method Details

getSingleCellDimension

SingleCellDimension getSingleCellDimension(Collection<BioAssay> bioAssays)
                                    throws IOException,
IllegalArgumentException

Load the single-cell dimension present in the data.

Not all samples might be present and thus the returned SingleCellDimension will have a expression data for a subset of the data.

Parameters:

bioAssays - a set of bioassays to use when populating the dimension, not all bioassays may be used

Throws:

IllegalArgumentException - if a sample present in the data cannot be matched to one of the supplied BioAssay, ignored if DataLoader.setIgnoreUnmatchedSamples(boolean) is set to true.

IOException

getCellTypeAssignments

Set<CellTypeAssignment> getCellTypeAssignments(SingleCellDimension dimension)
                                        throws IOException

Load single-cell type assignments present in the data.

Throws:

IOException

getOtherCellLevelCharacteristics

Set<CellLevelCharacteristics> getOtherCellLevelCharacteristics(SingleCellDimension dimension)
                                                        throws IOException

Load cell-level characteristics that are not cell type assignments present in the data.

Throws:

IOException

getSequencingMetadata

Map<BioAssay,SequencingMetadata> getSequencingMetadata(SingleCellDimension dimension)
                                                throws IOException

Throws:

IOException

loadVectors

Stream<SingleCellExpressionDataVector> loadVectors(Collection<CompositeSequence> designElements,
 SingleCellDimension dimension,
 QuantitationType quantitationType)
                                            throws IOException,
IllegalArgumentException

Produces a stream of single-cell expression data vectors for the given QuantitationType.

Parameters:

designElements - a collection of design elements for mapping of element names used in the dataset to CompositeSequence

dimension - a dimension to use for creating vectors, may be loaded from the single-cell data with getSingleCellDimension(Collection)

quantitationType - a quantitation type to extract from the data for, may be loaded from the single-cell data with DataLoader.getQuantitationTypes()

Returns:

a stream of single-cell expression data vectors that must be closed when done, preferably using a try-with-resource block.

Throws:

IllegalArgumentException - if a design element present in the data cannot be matched to one of the supplied elements, requires setting DataLoader.setIgnoreUnmatchedDesignElements(boolean) to false

IOException