Package ubic.gemma.core.analysis.singleCell.aggregate

Class SingleCellAggregationConfig

java.lang.Object

ubic.gemma.core.analysis.singleCell.aggregate.SingleCellAggregationConfig

public class SingleCellAggregationConfig
extends Object

Configuration for aggregating single-cell data.

Author:

poirigui

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	SingleCellAggregationConfig.SingleCellAggregationConfigBuilder

Method Summary

Modifier and Type	Method	Description
static SingleCellAggregationConfig.SingleCellAggregationConfigBuilder	builder()
CellLevelCharacteristics	getMask()	Categorical mask to use on data.
boolean	isAdjustLibrarySizes()	Perform adjustment of library sizes to better reflect the number of reads in the source sample.
boolean	isIncludeMaskedCellsInLibrarySize()	Include masked cells in the library size calculation.
boolean	isMakePreferred()	Make the resulting QT preferred.

Methods inherited from class java.lang.Object

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

Method Details

builder

public static SingleCellAggregationConfig.SingleCellAggregationConfigBuilder builder()

getMask

@Nullable
public CellLevelCharacteristics getMask()

Categorical mask to use on data.

The category of the characteristics must be Categories.MASK.

isMakePreferred

public boolean isMakePreferred()

Make the resulting QT preferred.

isAdjustLibrarySizes

public boolean isAdjustLibrarySizes()

Perform adjustment of library sizes to better reflect the number of reads in the source sample.

isIncludeMaskedCellsInLibrarySize

public boolean isIncludeMaskedCellsInLibrarySize()

Include masked cells in the library size calculation.

The default is to exclude them as if they were simply filtered out.