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

Interface SingleCellExpressionExperimentSplitAndAggregateService

All Known Implementing Classes:

SingleCellExpressionExperimentSplitAndAggregateServiceImpl

public interface SingleCellExpressionExperimentSplitAndAggregateService

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

This allows for splitting and aggregating single-cell data in a single transaction. It also support re-aggregation

Author:

poirigui

See Also:

SingleCellExpressionExperimentSplitService, SingleCellExpressionExperimentSplitAndAggregateService

Method Summary

Modifier and Type	Method	Description
QuantitationType	redoAggregate(ExpressionExperiment expressionExperiment, QuantitationType scQt, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic,FactorValue> c2f, BioAssayDimension dimension, QuantitationType previousQt, AggregateConfig config)	Re-aggregate a dataset by any cell-level characteristics.
QuantitationType	redoAggregateByCellType(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, QuantitationType previousQt, AggregateConfig config)	Re-aggregate a dataset by cell type.
QuantitationType	splitAndAggregate(ExpressionExperiment expressionExperiment, QuantitationType scQt, CellLevelCharacteristics cta, ExperimentalFactor cellTypeFactor, Map<Characteristic,FactorValue> c2f, SplitConfig splitConfig, AggregateConfig config)	Split and aggregate by any cell-level characteristics.
QuantitationType	splitAndAggregateByCellType(ExpressionExperiment expressionExperiment, SplitConfig splitConfig, AggregateConfig config)	Split and aggregate by cell type.

Method Detail

splitAndAggregateByCellType

QuantitationType splitAndAggregateByCellType(ExpressionExperiment expressionExperiment,
                                             SplitConfig splitConfig,
                                             AggregateConfig config)

Split and aggregate by cell type.

See Also:

SingleCellExpressionExperimentSplitService.splitByCellType(ExpressionExperiment, SplitConfig), SingleCellExpressionExperimentAggregatorService.aggregateVectorsByCellType(ExpressionExperiment, List, AggregateConfig)

splitAndAggregate

QuantitationType splitAndAggregate(ExpressionExperiment expressionExperiment,
                                   QuantitationType scQt,
                                   CellLevelCharacteristics cta,
                                   ExperimentalFactor cellTypeFactor,
                                   Map<Characteristic,FactorValue> c2f,
                                   SplitConfig splitConfig,
                                   AggregateConfig config)

Split and aggregate by any cell-level characteristics.

See Also:

SingleCellExpressionExperimentSplitService.split(ExpressionExperiment, CellLevelCharacteristics, ExperimentalFactor, Map, SplitConfig), SingleCellExpressionExperimentAggregatorService.aggregateVectors(ExpressionExperiment, QuantitationType, List, CellLevelCharacteristics, ExperimentalFactor, Map, AggregateConfig)

redoAggregateByCellType

QuantitationType redoAggregateByCellType(ExpressionExperiment expressionExperiment,
                                         BioAssayDimension dimension,
                                         @Nullable
                                         QuantitationType previousQt,
                                         AggregateConfig 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:

SingleCellExpressionExperimentAggregatorService.aggregateVectorsByCellType(ExpressionExperiment, List, AggregateConfig)

redoAggregate

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

SingleCellExpressionExperimentAggregatorService.aggregateVectors(ExpressionExperiment, QuantitationType, List, CellLevelCharacteristics, ExperimentalFactor, Map, AggregateConfig)