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

Interface SingleCellExpressionExperimentSubSetService

All Known Implementing Classes:

SingleCellExpressionExperimentSubSetServiceImpl

public interface SingleCellExpressionExperimentSubSetService

Service to create single-cell expression experiment subsets.

Author:

poirigui

Method Summary

Modifier and Type	Method	Description
List<ExpressionExperimentSubSet>	createSubSets(ExpressionExperiment ee, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic,FactorValue> cellTypeMapping, 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

Method Details

createSubSetsByCellType

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
List<ExpressionExperimentSubSet> createSubSetsByCellType(ExpressionExperiment ee,
 SingleCellExperimentSubSetsCreationConfig config)

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.

Throws:

IllegalStateException - if there is no preferred cell type assignment, no (or multiple) cell type factor

createSubSets

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
List<ExpressionExperimentSubSet> createSubSets(ExpressionExperiment ee,
 CellLevelCharacteristics clc,
 ExperimentalFactor factor,
 Map<Characteristic,FactorValue> cellTypeMapping,
 SingleCellExperimentSubSetsCreationConfig config)

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

Returns:

a list of subsets representing subpopulations of cells