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

Class MexSingleCellDataLoader

java.lang.Object

ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoader

All Implemented Interfaces:

Closeable, AutoCloseable, DataLoader, SequencingDataLoader, SingleCellDataLoader

public class MexSingleCellDataLoader
extends Object
implements SingleCellDataLoader

Load single cell data from 10X Genomics MEX format.

Author:

poirigui

Constructor Summary

Constructors

Constructor	Description
MexSingleCellDataLoader(List<String> sampleNames, List<Path> barcodeFiles, List<Path> genesFiles, List<Path> matrixFiles)

Method Summary

Modifier and Type	Method	Description
void	close()	Free any resources that the loaded has setup.
float[]	double2float(double[] vec)
int[]	double2int(double[] vec)
long[]	double2long(double[] vec)
Set<CellTypeAssignment>	getCellTypeAssignments(SingleCellDimension dimension)	MEX does not provide cell type labels.
Set<ExperimentalFactor>	getFactors(Collection<BioAssay> samples, Map<BioMaterial,Set<FactorValue>> factorValueAssignments)	MEX does not provide experimental factors.
Set<String>	getGenes()	Load gene identifiers present in the data.
Set<CellLevelCharacteristics>	getOtherCellLevelCharacteristics(SingleCellDimension dimension)	Load cell-level characteristics that are not cell type assignments present in the data.
Set<QuantitationType>	getQuantitationTypes()	Load quantitation types present in the data.
Set<String>	getSampleNames()	Obtain the sample names present in the data.
Map<BioMaterial,Set<Characteristic>>	getSamplesCharacteristics(Collection<BioAssay> samples)	MEX does not provide sample characteristics.
Map<BioAssay,SequencingMetadata>	getSequencingMetadata(Collection<BioAssay> samples)	Retrieve various sequencing metadata if counting data is present.
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 scd, QuantitationType quantitationType)	Produces a stream of single-cell expression data vectors for the given QuantitationType.
void	setAllowMappingDesignElementsToGeneSymbols(boolean allowMappingDesignElementsToGeneSymbols)	Allow mapping probe to gene symbols.
void	setBioAssayToSampleNameMapper(BioAssayMapper bioAssayToSampleNameMapper)	Set the strategy used for mapping BioAssay to sample names from the data.
void	setDesignElementToGeneMapper(DesignElementMapper designElementToGeneMapper)	Set the strategy used for mapping CompositeSequence to gene identifiers from the data.
void	setDiscardEmptyCells(boolean discardEmptyCells)	Discard empty cells by removing columns from MTX file that have no gene-associated counts.
void	setIgnoreUnmatchedDesignElements(boolean ignoreUnmatchedDesignElements)	Ignore unmatched design elements from the data when creating vectors.
void	setIgnoreUnmatchedSamples(boolean ignoreUnmatchedSamples)	Ignore unmatched samples from the data.
void	setUseDoublePrecision(boolean useDoublePrecision)	Use double precision (i.e.

Methods inherited from class java.lang.Object

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

Constructor Details

MexSingleCellDataLoader

public MexSingleCellDataLoader(List<String> sampleNames,
 List<Path> barcodeFiles,
 List<Path> genesFiles,
 List<Path> matrixFiles)

Method Details

getSampleNames

public Set<String> getSampleNames()

Description copied from interface: DataLoader

Obtain the sample names present in the data.

Specified by:

getSampleNames in interface DataLoader

getSingleCellDimension

public SingleCellDimension getSingleCellDimension(Collection<BioAssay> bioAssays)
                                           throws IOException

Description copied from interface: SingleCellDataLoader

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.

Specified by:

getSingleCellDimension in interface SingleCellDataLoader

Parameters:

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

Throws:

IOException

getQuantitationTypes

public Set<QuantitationType> getQuantitationTypes()
                                           throws IOException

Description copied from interface: DataLoader

Load quantitation types present in the data.

Specified by:

getQuantitationTypes in interface DataLoader

Throws:

IOException

getCellTypeAssignments

public Set<CellTypeAssignment> getCellTypeAssignments(SingleCellDimension dimension)

MEX does not provide cell type labels.

Specified by:

getCellTypeAssignments in interface SingleCellDataLoader

getOtherCellLevelCharacteristics

public Set<CellLevelCharacteristics> getOtherCellLevelCharacteristics(SingleCellDimension dimension)

Description copied from interface: SingleCellDataLoader

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

Specified by:

getOtherCellLevelCharacteristics in interface SingleCellDataLoader

getFactors

public Set<ExperimentalFactor> getFactors(Collection<BioAssay> samples,
 @Nullable
 Map<BioMaterial,Set<FactorValue>> factorValueAssignments)

MEX does not provide experimental factors.

Specified by:

getFactors in interface DataLoader

Parameters:

samples - samples to use when determining which factors to load

factorValueAssignments - if non-null, the proposed assignment of factor values to samples are populated in the mapping.

Returns:

a set of factors present in the data

getSamplesCharacteristics

public Map<BioMaterial,Set<Characteristic>> getSamplesCharacteristics(Collection<BioAssay> samples)

MEX does not provide sample characteristics.

Specified by:

getSamplesCharacteristics in interface DataLoader

Parameters:

samples - to use when determining which characteristics to load

Returns:

proposed characteristics grouped by sample

getGenes

public Set<String> getGenes()
                     throws IOException

Description copied from interface: DataLoader

Load gene identifiers present in the data.

Specified by:

getGenes in interface DataLoader

Throws:

IOException

getSequencingMetadata

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

Specified by:

getSequencingMetadata in interface SingleCellDataLoader

Throws:

IOException

getSequencingMetadata

public Map<BioAssay,SequencingMetadata> getSequencingMetadata(Collection<BioAssay> samples)
                                                       throws IOException

Description copied from interface: SequencingDataLoader

Retrieve various sequencing metadata if counting data is present.

Specified by:

getSequencingMetadata in interface SequencingDataLoader

Throws:

IOException

loadVectors

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

Description copied from interface: SingleCellDataLoader

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

Specified by:

loadVectors in interface SingleCellDataLoader

Parameters:

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

scd - a dimension to use for creating vectors, may be loaded from the single-cell data with SingleCellDataLoader.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:

IOException

close

public void close()
           throws IOException

Description copied from interface: DataLoader

Free any resources that the loaded has setup.

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable

Specified by:

close in interface DataLoader

Throws:

IOException

double2float

public float[] double2float(double[] vec)

double2int

public int[] double2int(double[] vec)

double2long

public long[] double2long(double[] vec)

setBioAssayToSampleNameMapper

public void setBioAssayToSampleNameMapper(BioAssayMapper bioAssayToSampleNameMapper)

Description copied from interface: DataLoader

Set the strategy used for mapping BioAssay to sample names from the data.

Specified by:

setBioAssayToSampleNameMapper in interface DataLoader

setIgnoreUnmatchedSamples

public void setIgnoreUnmatchedSamples(boolean ignoreUnmatchedSamples)

Description copied from interface: DataLoader

Ignore unmatched samples from the data.

This defaults to true.

Specified by:

setIgnoreUnmatchedSamples in interface DataLoader

setDesignElementToGeneMapper

public void setDesignElementToGeneMapper(DesignElementMapper designElementToGeneMapper)

Description copied from interface: DataLoader

Set the strategy used for mapping CompositeSequence to gene identifiers from the data.

Specified by:

setDesignElementToGeneMapper in interface DataLoader

setIgnoreUnmatchedDesignElements

public void setIgnoreUnmatchedDesignElements(boolean ignoreUnmatchedDesignElements)

Description copied from interface: DataLoader

Ignore unmatched design elements from the data when creating vectors.

This defaults to true.

There's a discussions to make this default in false in general for sequencing data.

Specified by:

setIgnoreUnmatchedDesignElements in interface DataLoader

setAllowMappingDesignElementsToGeneSymbols

public void setAllowMappingDesignElementsToGeneSymbols(boolean allowMappingDesignElementsToGeneSymbols)

Allow mapping probe to gene symbols.

This is used as fallback if the gene ID cannot be found in the supplied platform. If this is set to true, the second column of the genes file will be looked up.

setUseDoublePrecision

public void setUseDoublePrecision(boolean useDoublePrecision)

Use double precision (i.e. PrimitiveType.DOUBLE for real numbers and PrimitiveType.LONG for integers.

setDiscardEmptyCells

public void setDiscardEmptyCells(boolean discardEmptyCells)

Discard empty cells by removing columns from MTX file that have no gene-associated counts.

This can be disabled for faster loading.