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

Class MexSingleCellDataLoaderConfig

java.lang.Object

ubic.gemma.core.loader.expression.DataLoaderConfig

ubic.gemma.core.loader.expression.sequencing.SequencingDataLoaderConfig

ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig

ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderConfig

public class MexSingleCellDataLoaderConfig
extends SingleCellDataLoaderConfig

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	MexSingleCellDataLoaderConfig.MexSingleCellDataLoaderConfigBuilder<C extends MexSingleCellDataLoaderConfig,B extends MexSingleCellDataLoaderConfig.MexSingleCellDataLoaderConfigBuilder<C,B>>

Nested classes/interfaces inherited from class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig

SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder<C extends SingleCellDataLoaderConfig,B extends SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder<C,B>>

Nested classes/interfaces inherited from class ubic.gemma.core.loader.expression.sequencing.SequencingDataLoaderConfig

SequencingDataLoaderConfig.SequencingDataLoaderConfigBuilder<C extends SequencingDataLoaderConfig,B extends SequencingDataLoaderConfig.SequencingDataLoaderConfigBuilder<C,B>>

Nested classes/interfaces inherited from class ubic.gemma.core.loader.expression.DataLoaderConfig

DataLoaderConfig.DataLoaderConfigBuilder<C extends DataLoaderConfig,B extends DataLoaderConfig.DataLoaderConfigBuilder<C,B>>

Field Summary

Fields inherited from class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig

transformExecutor

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	MexSingleCellDataLoaderConfig(MexSingleCellDataLoaderConfig.MexSingleCellDataLoaderConfigBuilder<?,?> b)

Method Summary

Modifier and Type	Method	Description
static MexSingleCellDataLoaderConfig.MexSingleCellDataLoaderConfigBuilder<?,?>	builder()
Boolean	getApply10xFilter()	Filter 10x MEX data to remove low-quality cells.
String	getUse10xChemistry()	Chemistry used for single-cell sequencing.
boolean	isAllowMappingDesignElementsToGeneSymbols()
boolean	isUseDoublePrecision()	Use double precision for loading MEX data.

Methods inherited from class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig

getCellTypeAssignmentDescription, getCellTypeAssignmentFile, getCellTypeAssignmentName, getCellTypeAssignmentProtocol, getOtherCellLevelCharacteristicsFile, getOtherCellLevelCharacteristicsNames, getPreferredCellTypeAssignmentName, getTransformExecutor, isIgnoreSamplesLackingData, isIgnoreUnmatchedCellIds, isInferSamplesFromCellIdsOverlap, isMarkSingleCellTypeAssignmentAsPreferred, isPreferSinglePrecision, isReplaceExistingCellTypeAssignment, isReplaceExistingOtherCellLevelCharacteristics, isSkipTransformations, isUseCellIdsIfSampleNameIsMissing

Methods inherited from class ubic.gemma.core.loader.expression.sequencing.SequencingDataLoaderConfig

getDefaultSequencingMetadata, getSequencingMetadataFile

Methods inherited from class ubic.gemma.core.loader.expression.DataLoaderConfig

getDataPath, getQuantitationTypeName, getQuantitationTypeNewName, getQuantitationTypeNewScaleType, getQuantitationTypeNewType, getRenamingFile, isMarkQuantitationTypeAsPreferred, isMarkQuantitationTypeAsRecomputedFromRawData, isReplaceExistingQuantitationType

Methods inherited from class java.lang.Object

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

Constructor Details

MexSingleCellDataLoaderConfig

protected MexSingleCellDataLoaderConfig(MexSingleCellDataLoaderConfig.MexSingleCellDataLoaderConfigBuilder<?,?> b)

Method Details

builder

public static MexSingleCellDataLoaderConfig.MexSingleCellDataLoaderConfigBuilder<?,?> builder()

isAllowMappingDesignElementsToGeneSymbols

public boolean isAllowMappingDesignElementsToGeneSymbols()

getApply10xFilter

@Nullable
public Boolean getApply10xFilter()

Filter 10x MEX data to remove low-quality cells.

Default is to auto-detect.

If set to true, the filter will be applied to every sample. If set to null, detection logic will be applied on a per-sample basis. If set to false, no filtering will be performed.

This should only be applied to unfiltered MEX data from 10x Chromium platform.

See Also:

• SingleCell10xMexFilter

getUse10xChemistry

@Nullable
public String getUse10xChemistry()

Chemistry used for single-cell sequencing.

This affects the 10x MEX data filter.

Default is to auto-detect.

See Also:

• SingleCell10xMexFilter

isUseDoublePrecision

public boolean isUseDoublePrecision()

Use double precision for loading MEX data.

Default is to use single precision for storage efficiency.

See Also:

• MexSingleCellDataLoader.setUseDoublePrecision(boolean)