Package ubic.gemma.core.analysis.singleCell

Class SingleCellSparsityMetrics

java.lang.Object

ubic.gemma.core.analysis.singleCell.SingleCellSparsityMetrics

public class SingleCellSparsityMetrics
extends Object

Compute sparsity metrics for single-cell data.

Author:

poirigui

Constructor Summary

Constructors

Constructor	Description
SingleCellSparsityMetrics()

Method Summary

Modifier and Type	Method	Description
static void	addExpressedCells(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int characteristicIndex, boolean[] mask, boolean[] isExpressed)	Populate a boolean vector that indicates if a cell has at least one expressed gene.
static int	getNumberOfCells(Collection<SingleCellExpressionDataVector> vectors, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int characteristicIndex, boolean[] mask)	Calculate the number of cells with at least one gene expressed.
static int	getNumberOfCellsByDesignElements(Collection<SingleCellExpressionDataVector> vectors, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int characteristicIndex, boolean[] mask)	Calculate the number of expressed cell by gene pairs.
static int	getNumberOfCellsByDesignElements(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int characteristicIndex, boolean[] mask)
static int	getNumberOfDesignElements(Collection<SingleCellExpressionDataVector> vectors, int sampleIndex, CellLevelCharacteristics characteristic, int characteristicIndex, boolean[] mask)	Calculate the number of genes expressed in at least one cell.
static int	getNumberOfDesignElements(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics characteristic, int characteristicIndex, boolean[] mask)
static boolean	isExpressed(double value, ScaleType scaleType)	Check if a value is expressed on a given scale.
static boolean	isSupported(SingleCellExpressionDataVector vector)	Check if sparsity metrics can be computed for a given collection of vectors.

Methods inherited from class java.lang.Object

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

Constructor Details

SingleCellSparsityMetrics

public SingleCellSparsityMetrics()

Method Details

isSupported

public static boolean isSupported(SingleCellExpressionDataVector vector)

Check if sparsity metrics can be computed for a given collection of vectors.

getNumberOfCells

public static int getNumberOfCells(Collection<SingleCellExpressionDataVector> vectors,
 int sampleIndex,
 @Nullable
 CellLevelCharacteristics cellLevelCharacteristics,
 int characteristicIndex,
 @Nullable
 boolean[] mask)

Calculate the number of cells with at least one gene expressed.

Parameters:

characteristicIndex - only cell with the given characteristic index will be considered

addExpressedCells

public static void addExpressedCells(SingleCellExpressionDataVector vector,
 int sampleIndex,
 @Nullable
 CellLevelCharacteristics cellLevelCharacteristics,
 int characteristicIndex,
 @Nullable
 boolean[] mask,
 boolean[] isExpressed)

Populate a boolean vector that indicates if a cell has at least one expressed gene.

getNumberOfDesignElements

public static int getNumberOfDesignElements(Collection<SingleCellExpressionDataVector> vectors,
 int sampleIndex,
 @Nullable
 CellLevelCharacteristics characteristic,
 int characteristicIndex,
 @Nullable
 boolean[] mask)

Calculate the number of genes expressed in at least one cell.

getNumberOfDesignElements

public static int getNumberOfDesignElements(SingleCellExpressionDataVector vector,
 int sampleIndex,
 @Nullable
 CellLevelCharacteristics characteristic,
 int characteristicIndex,
 @Nullable
 boolean[] mask)

getNumberOfCellsByDesignElements

public static int getNumberOfCellsByDesignElements(Collection<SingleCellExpressionDataVector> vectors,
 int sampleIndex,
 @Nullable
 CellLevelCharacteristics cellLevelCharacteristics,
 int characteristicIndex,
 @Nullable
 boolean[] mask)

Calculate the number of expressed cell by gene pairs.

getNumberOfCellsByDesignElements

public static int getNumberOfCellsByDesignElements(SingleCellExpressionDataVector vector,
 int sampleIndex,
 @Nullable
 CellLevelCharacteristics cellLevelCharacteristics,
 int characteristicIndex,
 @Nullable
 boolean[] mask)

isExpressed

public static boolean isExpressed(double value,
 ScaleType scaleType)

Check if a value is expressed on a given scale.