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

Interface SingleCellExpressionExperimentCreateSubSetsAndAggregateService

All Known Implementing Classes:

SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceImpl

public interface SingleCellExpressionExperimentCreateSubSetsAndAggregateService

High-level service for creating subsets and aggregating single-cell expression experiments.

This allows for subsetting and aggregating single-cell data in a single transaction. It also supports re-aggregation from an existing subset structure.

Author:

poirigui

See Also:

• SingleCellExpressionExperimentSubSetService
• SingleCellExpressionExperimentCreateSubSetsAndAggregateService

Method Summary

Modifier and Type	Method	Description
QuantitationType	createSubSetsAndAggregate(ExpressionExperiment expressionExperiment, QuantitationType scQt, CellLevelCharacteristics cta, ExperimentalFactor cellTypeFactor, Map<Characteristic,FactorValue> c2f, SingleCellExperimentSubSetsCreationConfig singleCellExperimentSubSetsCreationConfig, SingleCellAggregationConfig config)	Create subsets and aggregate by any cell-level characteristics.
QuantitationType	createSubSetsAndAggregateByCellType(ExpressionExperiment expressionExperiment, SingleCellExperimentSubSetsCreationConfig singleCellExperimentSubSetsCreationConfig, SingleCellAggregationConfig config)	Create subsets and aggregate by cell type.
QuantitationType	redoAggregate(ExpressionExperiment expressionExperiment, QuantitationType scQt, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic,FactorValue> c2f, BioAssayDimension dimension, QuantitationType previousQt, SingleCellAggregationConfig config)	Re-aggregate a dataset by any cell-level characteristics.
QuantitationType	redoAggregateByCellType(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, QuantitationType previousQt, SingleCellAggregationConfig config)	Re-aggregate a dataset by cell type.

Method Details

createSubSetsAndAggregateByCellType

QuantitationType createSubSetsAndAggregateByCellType(ExpressionExperiment expressionExperiment,
 SingleCellExperimentSubSetsCreationConfig singleCellExperimentSubSetsCreationConfig,
 SingleCellAggregationConfig config)

Create subsets and aggregate by cell type.

See Also:

• SingleCellExpressionExperimentSubSetService.createSubSetsByCellType(ExpressionExperiment, SingleCellExperimentSubSetsCreationConfig)
• SingleCellExpressionExperimentAggregateService.aggregateVectorsByCellType(ExpressionExperiment, List, SingleCellAggregationConfig)

createSubSetsAndAggregate

QuantitationType createSubSetsAndAggregate(ExpressionExperiment expressionExperiment,
 QuantitationType scQt,
 CellLevelCharacteristics cta,
 ExperimentalFactor cellTypeFactor,
 Map<Characteristic,FactorValue> c2f,
 SingleCellExperimentSubSetsCreationConfig singleCellExperimentSubSetsCreationConfig,
 SingleCellAggregationConfig config)

Create subsets and aggregate by any cell-level characteristics.

See Also:

• SingleCellExpressionExperimentSubSetService.createSubSets(ExpressionExperiment, CellLevelCharacteristics, ExperimentalFactor, Map, SingleCellExperimentSubSetsCreationConfig)
• SingleCellExpressionExperimentAggregateService.aggregateVectors(ExpressionExperiment, QuantitationType, List, CellLevelCharacteristics, ExperimentalFactor, Map, SingleCellAggregationConfig)

redoAggregateByCellType

QuantitationType redoAggregateByCellType(ExpressionExperiment expressionExperiment,
 BioAssayDimension dimension,
 @Nullable
 QuantitationType previousQt,
 SingleCellAggregationConfig config)

Re-aggregate a dataset by cell type.

Parameters:

dimension - a dimension to reuse for aggregating

previousQt - a previous quantitation type the re-aggregated one is replacing, it will be removed prior to the new one being added. Ignored if null.

See Also:

• SingleCellExpressionExperimentAggregateService.aggregateVectorsByCellType(ExpressionExperiment, List, SingleCellAggregationConfig)

redoAggregate

QuantitationType redoAggregate(ExpressionExperiment expressionExperiment,
 QuantitationType scQt,
 CellLevelCharacteristics clc,
 ExperimentalFactor factor,
 Map<Characteristic,FactorValue> c2f,
 BioAssayDimension dimension,
 @Nullable
 QuantitationType previousQt,
 SingleCellAggregationConfig config)

Re-aggregate a dataset by any cell-level characteristics.

Parameters:

dimension - a dimension to reuse for aggregating

previousQt - a previous quantitation type the re-aggregated one is replacing, it will be removed prior to the new one being added. Ignored if null.

See Also:

• SingleCellExpressionExperimentAggregateService.aggregateVectors(ExpressionExperiment, QuantitationType, List, CellLevelCharacteristics, ExperimentalFactor, Map, SingleCellAggregationConfig)