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

Class SingleCellExpressionExperimentSplitServiceImpl

java.lang.Object

ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentSplitServiceImpl

All Implemented Interfaces:

SingleCellExpressionExperimentSplitService

@Service
public class SingleCellExpressionExperimentSplitServiceImpl
extends Object
implements SingleCellExpressionExperimentSplitService

Constructor Summary

Constructors

Constructor	Description
SingleCellExpressionExperimentSplitServiceImpl()

Method Summary

Modifier and Type	Method	Description
List<ExpressionExperimentSubSet>	split(ExpressionExperiment ee, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic,FactorValue> mappedCellTypeFactors, SplitConfig config)	Split biomaterials and bioassays by the given CellLevelCharacteristics.
List<ExpressionExperimentSubSet>	splitByCellType(ExpressionExperiment ee, SplitConfig config)	Split a single-cell dataset by cell type.

Methods inherited from class java.lang.Object

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

Constructor Detail

SingleCellExpressionExperimentSplitServiceImpl

public SingleCellExpressionExperimentSplitServiceImpl()

Method Detail

splitByCellType

@Transactional
public List<ExpressionExperimentSubSet> splitByCellType(ExpressionExperiment ee,
                                                        SplitConfig config)

Description copied from interface: SingleCellExpressionExperimentSplitService

Split a single-cell dataset by cell type.

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

Specified by:

splitByCellType in interface SingleCellExpressionExperimentSplitService

split

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

Description copied from interface: SingleCellExpressionExperimentSplitService

Split 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:

split in interface SingleCellExpressionExperimentSplitService

Returns:

a list of subsets representing subpopulations of cells