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

Class MexSingleCellDataLoaderConfig.MexSingleCellDataLoaderConfigBuilder<C extends MexSingleCellDataLoaderConfig,B extends MexSingleCellDataLoaderConfig.MexSingleCellDataLoaderConfigBuilder<C,B>>

java.lang.Object

ubic.gemma.core.loader.expression.DataLoaderConfig.DataLoaderConfigBuilder<C,B>

ubic.gemma.core.loader.expression.sequencing.SequencingDataLoaderConfig.SequencingDataLoaderConfigBuilder<C,B>

ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder<C,B>

ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderConfig.MexSingleCellDataLoaderConfigBuilder<C,B>

Enclosing class:

MexSingleCellDataLoaderConfig

public abstract static class MexSingleCellDataLoaderConfig.MexSingleCellDataLoaderConfigBuilder<C extends MexSingleCellDataLoaderConfig,B extends MexSingleCellDataLoaderConfig.MexSingleCellDataLoaderConfigBuilder<C,B>>
extends SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder<C,B>

Constructor Summary

Constructors

Constructor	Description
MexSingleCellDataLoaderConfigBuilder()

Method Summary

Modifier and Type	Method	Description
B	allowMappingDesignElementsToGeneSymbols(boolean allowMappingDesignElementsToGeneSymbols)
B	apply10xFilter(Boolean apply10xFilter)	Filter 10x MEX data to remove low-quality cells.
abstract C	build()
protected abstract B	self()
String	toString()
B	use10xChemistry(String use10xChemistry)	Chemistry used for single-cell sequencing.
B	useDoublePrecision(boolean useDoublePrecision)	Use double precision for loading MEX data.

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

cellTypeAssignmentDescription, cellTypeAssignmentFile, cellTypeAssignmentName, cellTypeAssignmentProtocol, ignoreSamplesLackingData, ignoreUnmatchedCellIds, inferSamplesFromCellIdsOverlap, markSingleCellTypeAssignmentAsPreferred, otherCellLevelCharacteristicsFile, otherCellLevelCharacteristicsNames, preferredCellTypeAssignmentName, preferSinglePrecision, replaceExistingCellTypeAssignment, replaceExistingOtherCellLevelCharacteristics, skipTransformations, transformExecutor, useCellIdsIfSampleNameIsMissing

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

defaultSequencingMetadata, sequencingMetadataFile

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

dataPath, markQuantitationTypeAsPreferred, markQuantitationTypeAsRecomputedFromRawData, quantitationTypeName, quantitationTypeNewName, quantitationTypeNewScaleType, quantitationTypeNewType, renamingFile, replaceExistingQuantitationType

Methods inherited from class java.lang.Object

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

Constructor Details

MexSingleCellDataLoaderConfigBuilder

public MexSingleCellDataLoaderConfigBuilder()

Method Details

allowMappingDesignElementsToGeneSymbols

public B allowMappingDesignElementsToGeneSymbols(boolean allowMappingDesignElementsToGeneSymbols)

Returns:

this.

apply10xFilter

public B apply10xFilter(@Nullable
 Boolean apply10xFilter)

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.

Returns:

this.

See Also:

• SingleCell10xMexFilter

use10xChemistry

public B use10xChemistry(@Nullable
 String use10xChemistry)

Chemistry used for single-cell sequencing.

This affects the 10x MEX data filter.

Default is to auto-detect.

Returns:

this.

See Also:

• SingleCell10xMexFilter

useDoublePrecision

public B useDoublePrecision(boolean useDoublePrecision)

Use double precision for loading MEX data.

Default is to use single precision for storage efficiency.

Returns:

this.

See Also:

• MexSingleCellDataLoader.setUseDoublePrecision(boolean)

self

protected abstract B self()

Specified by:

self in class SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder<C extends MexSingleCellDataLoaderConfig,B extends MexSingleCellDataLoaderConfig.MexSingleCellDataLoaderConfigBuilder<C,B>>

build

public abstract C build()

Specified by:

build in class SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder<C extends MexSingleCellDataLoaderConfig,B extends MexSingleCellDataLoaderConfig.MexSingleCellDataLoaderConfigBuilder<C,B>>

toString

public String toString()

Overrides:

toString in class SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder<C extends MexSingleCellDataLoaderConfig,B extends MexSingleCellDataLoaderConfig.MexSingleCellDataLoaderConfigBuilder<C,B>>