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

Interface SingleCellExpressionExperimentSplitService

All Known Implementing Classes:

SingleCellExpressionExperimentSplitServiceImpl

public interface SingleCellExpressionExperimentSplitService

Split a single-cell expression experiment into sub-experiments by cell type.

Author:

poirigui

Method Summary

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

Method Details

splitByCellType

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

Split a single-cell dataset by cell type.

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

split

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

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

Returns:

a list of subsets representing subpopulations of cells