Package ubic.gemma.core.analysis.singleCell

Class SingleCellSparsityMetrics

java.lang.Object

ubic.gemma.core.analysis.singleCell.SingleCellSparsityMetrics

@Component
public class SingleCellSparsityMetrics
extends Object

Compute sparsity metrics for single cell data.

Author:

poirigui

Field Summary

Fields

Modifier and Type	Field	Description
static final double	DEFAULT_THRESHOLD	Default threshold to use when determining if a value is expressed.

Constructor Summary

Constructors

Constructor	Description
SingleCellSparsityMetrics()
SingleCellSparsityMetrics(double threshold)

Method Summary

Modifier and Type	Method	Description
void	addExpressedCells(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int characteristicIndex, boolean[] isExpressed)	Populate a boolean vector that indicates if a cell has at least one expressed gene.
int	getNumberOfCells(Collection<SingleCellExpressionDataVector> vectors, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int characteristicIndex)	Calculate the number of cells with at least one gene expressed.
int	getNumberOfCellsByDesignElements(Collection<SingleCellExpressionDataVector> vectors, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int characteristicIndex)	Calculate the number of expressed cell by gene pairs.
int	getNumberOfCellsByDesignElements(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int characteristicIndex)
int	getNumberOfDesignElements(Collection<SingleCellExpressionDataVector> vectors, int sampleIndex, CellLevelCharacteristics characteristic, int characteristicIndex)	Calculate the number of genes expressed in at least one cell.
int	getNumberOfDesignElements(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics characteristic, int characteristicIndex)
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

Field Details

DEFAULT_THRESHOLD

public static final double DEFAULT_THRESHOLD

Default threshold to use when determining if a value is expressed.

See Also:

• Constant Field Values

Constructor Details

SingleCellSparsityMetrics

public SingleCellSparsityMetrics()

SingleCellSparsityMetrics

public SingleCellSparsityMetrics(double threshold)

Parameters:

threshold - exclusive value to use to assess if data on a ScaleType.LINEAR scale is expressed. The threshold is transformed depending on the scale type of the vectors being tested:

• ScaleType.COUNT uses Math.rint(double)
• ScaleType.LOG1P uses Math.log1p(double)
• ScaleType.LOG2 uses Math.log(double) / Math.log(2)
• ScaleType.LN uses Math.log(double)
• ScaleType.LOG10 uses Math.log10(double)

Note that for ScaleType.PERCENT, ScaleType.PERCENT1 and ScaleType.LOGBASEUNKNOWN, only zero is supported. If a scale type is not supported, an exception will be raised. You can use isSupported(SingleCellExpressionDataVector) to safely perform the check.

Method Details

isSupported

public boolean isSupported(SingleCellExpressionDataVector vector)

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

getNumberOfCells

public int getNumberOfCells(Collection<SingleCellExpressionDataVector> vectors,
 int sampleIndex,
 @Nullable
 CellLevelCharacteristics cellLevelCharacteristics,
 int characteristicIndex)

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

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

getNumberOfDesignElements

public int getNumberOfDesignElements(Collection<SingleCellExpressionDataVector> vectors,
 int sampleIndex,
 @Nullable
 CellLevelCharacteristics characteristic,
 int characteristicIndex)

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

getNumberOfDesignElements

public int getNumberOfDesignElements(SingleCellExpressionDataVector vector,
 int sampleIndex,
 @Nullable
 CellLevelCharacteristics characteristic,
 int characteristicIndex)

getNumberOfCellsByDesignElements

public int getNumberOfCellsByDesignElements(Collection<SingleCellExpressionDataVector> vectors,
 int sampleIndex,
 @Nullable
 CellLevelCharacteristics cellLevelCharacteristics,
 int characteristicIndex)

Calculate the number of expressed cell by gene pairs.

getNumberOfCellsByDesignElements

public int getNumberOfCellsByDesignElements(SingleCellExpressionDataVector vector,
 int sampleIndex,
 @Nullable
 CellLevelCharacteristics cellLevelCharacteristics,
 int characteristicIndex)