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

Class SingleCellExpressionExperimentSubSetServiceImpl

java.lang.Object

ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentSubSetServiceImpl

All Implemented Interfaces:

SingleCellExpressionExperimentSubSetService

@Service
public class SingleCellExpressionExperimentSubSetServiceImpl
extends Object
implements SingleCellExpressionExperimentSubSetService

Constructor Summary

Constructors

Constructor	Description
SingleCellExpressionExperimentSubSetServiceImpl()

Method Summary

Modifier and Type	Method	Description
List<ExpressionExperimentSubSet>	createSubSets(ExpressionExperiment ee, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic,FactorValue> mappedCellTypeFactors, SingleCellExperimentSubSetsCreationConfig config)	Subset biomaterials and bioassays by the given CellLevelCharacteristics.
List<ExpressionExperimentSubSet>	createSubSetsByCellType(ExpressionExperiment ee, SingleCellExperimentSubSetsCreationConfig config)	Subset a single-cell dataset by preferred cell type assignment the cell type factor and the

Methods inherited from class java.lang.Object

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

Constructor Details

SingleCellExpressionExperimentSubSetServiceImpl

public SingleCellExpressionExperimentSubSetServiceImpl()

Method Details

createSubSetsByCellType

@Transactional
public List<ExpressionExperimentSubSet> createSubSetsByCellType(ExpressionExperiment ee,
 SingleCellExperimentSubSetsCreationConfig config)

Description copied from interface: SingleCellExpressionExperimentSubSetService

Subset a single-cell dataset by preferred cell type assignment the cell type factor and the

The dataset must have a preferred CellTypeAssignment and a cell type factor in its experimental design.

Specified by:

createSubSetsByCellType in interface SingleCellExpressionExperimentSubSetService

createSubSets

@Transactional
public List<ExpressionExperimentSubSet> createSubSets(ExpressionExperiment ee,
 CellLevelCharacteristics clc,
 ExperimentalFactor factor,
 Map<Characteristic,FactorValue> mappedCellTypeFactors,
 SingleCellExperimentSubSetsCreationConfig config)

Description copied from interface: SingleCellExpressionExperimentSubSetService

Subset biomaterials and bioassays by the given CellLevelCharacteristics.

This method will:

• create sub-BioMaterials for each subject and cell type
• create corresponding BioAssays for the sub-BioMaterials
• attach the BioAssays to ExpressionExperimentSubSet

Specified by:

createSubSets in interface SingleCellExpressionExperimentSubSetService

Returns:

a list of subsets representing subpopulations of cells