Package ubic.gemma.core.analysis.singleCell

Class SingleCellSlicerUtils

java.lang.Object

ubic.gemma.core.analysis.singleCell.SingleCellSlicerUtils

public class SingleCellSlicerUtils
extends Object

Utilities for slicing single cell data.

Author:

poirigui

See Also:

BulkDataSlicerUtils

Constructor Summary

Constructors

Constructor	Description
SingleCellSlicerUtils()

Method Summary

Modifier and Type	Method	Description
static Function<SingleCellExpressionDataVector,SingleCellExpressionDataVector>	createSlicer(List<BioAssay> assays)	Create a slicer for single-cell data vectors.
static Function<SingleCellExpressionDataVector,SingleCellExpressionDataVector>	createSlicer(List<BioAssay> assays, List<String> cellIds, Set<CellTypeAssignment> ctas, Set<CellLevelCharacteristics> clcs)	Create a slicer for single-cell data vectors whose cell IDs, CTAs, and CLCs are already pre-sliced.
static Collection<SingleCellExpressionDataVector>	slice(Collection<SingleCellExpressionDataVector> vectors, List<BioAssay> bioAssays)
static List<String>	sliceCellIds(SingleCellDimension singleCellDimension, List<BioAssay> assays, int[] starts, int[] ends, int numCells)
static Set<CellLevelCharacteristics>	sliceClcs(SingleCellDimension singleCellDimension, List<BioAssay> assays, int[] starts, int[] ends, int numCells)
static Set<CellTypeAssignment>	sliceCtas(SingleCellDimension singleCellDimension, List<BioAssay> assays, int[] starts, int[] ends, int numCells)

Methods inherited from class java.lang.Object

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

Constructor Detail

SingleCellSlicerUtils

public SingleCellSlicerUtils()

Method Detail

slice

public static Collection<SingleCellExpressionDataVector> slice(Collection<SingleCellExpressionDataVector> vectors,
                                                               List<BioAssay> bioAssays)

createSlicer

public static Function<SingleCellExpressionDataVector,SingleCellExpressionDataVector> createSlicer(List<BioAssay> assays)

Create a slicer for single-cell data vectors.

createSlicer

public static Function<SingleCellExpressionDataVector,SingleCellExpressionDataVector> createSlicer(List<BioAssay> assays,
                                                                                                         @Nullable
                                                                                                         List<String> cellIds,
                                                                                                         @Nullable
                                                                                                         Set<CellTypeAssignment> ctas,
                                                                                                         @Nullable
                                                                                                         Set<CellLevelCharacteristics> clcs)

Create a slicer for single-cell data vectors whose cell IDs, CTAs, and CLCs are already pre-sliced.

Unlike sparse vectors, these structures can be sliced in the database.

Parameters:

cellIds - pre-sliced cell IDs

ctas - pre-sliced CTAs

clcs - pre-sliced CLCs

sliceCellIds

public static List<String> sliceCellIds(SingleCellDimension singleCellDimension,
                                        List<BioAssay> assays,
                                        int[] starts,
                                        int[] ends,
                                        int numCells)

sliceCtas

public static Set<CellTypeAssignment> sliceCtas(SingleCellDimension singleCellDimension,
                                                List<BioAssay> assays,
                                                int[] starts,
                                                int[] ends,
                                                int numCells)

sliceClcs

public static Set<CellLevelCharacteristics> sliceClcs(SingleCellDimension singleCellDimension,
                                                      List<BioAssay> assays,
                                                      int[] starts,
                                                      int[] ends,
                                                      int numCells)