Package ubic.gemma.core.analysis.singleCell

Class SingleCellDescriptive

java.lang.Object

ubic.gemma.core.analysis.singleCell.SingleCellDescriptive

public class SingleCellDescriptive
extends Object

Descriptive statistics for single cell data.

The utilities here extend DataVectorDescriptive by providing per-assay statistics.

Author:

poirigui

See Also:

• DataVectorDescriptive

Constructor Summary

Constructors

Constructor	Description
SingleCellDescriptive()

Method Summary

Modifier and Type	Method	Description
static int[]	count(SingleCellExpressionDataVector vector)	Count the number of values in each assay.
static int[]	countAboveThreshold(SingleCellExpressionDataVector vector, double threshold)	Compute the number of cells expressed strictly above the given threshold.
static int[]	countFast(SingleCellExpressionDataVector vector)	Quickly count the non-zeroes for each assay.
static int	countFast(SingleCellExpressionDataVector vector, int sampleIndex)
static int	countFast(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)
static int[]	countFast(SingleCellExpressionDataVector vector, CellLevelCharacteristics cellLevelCharacteristics)
static int[]	countFastWithUnknown(SingleCellExpressionDataVector vector, CellLevelCharacteristics cellLevelCharacteristics)
static double[]	max(SingleCellExpressionDataVector vector)
static double	max(SingleCellExpressionDataVector vector, int sampleIndex)
static double	max(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)
static double[]	max(SingleCellExpressionDataVector vector, CellLevelCharacteristics cellLevelCharacteristics)
static double[]	mean(SingleCellExpressionDataVector vector)	Calculate the mean of each assay for a given vector.
static double	mean(SingleCellExpressionDataVector vector, int sampleIndex)
static double	mean(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)
static double	mean(SingleCellExpressionDataVector vector, BioAssay sample)	Calculate the mean of a given assay.
static double[]	median(SingleCellExpressionDataVector vector)	Calculate the median of each assay for a given vector.
static double	median(SingleCellExpressionDataVector vector, int column)
static double	median(SingleCellExpressionDataVector vector, int column, CellLevelCharacteristics cellLevelCharacteristics, int row)
static double[]	min(SingleCellExpressionDataVector vector)
static double	min(SingleCellExpressionDataVector vector, int sampleIndex)
static double	min(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)
static double[]	min(SingleCellExpressionDataVector vector, CellLevelCharacteristics cellLevelCharacteristics)
static double[]	quantile(SingleCellExpressionDataVector vector, double q)
static double	quantile(SingleCellExpressionDataVector vector, int sampleIndex, double v)
static double	quantile(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row, double q)
static double[]	quantile(SingleCellExpressionDataVector vector, CellLevelCharacteristics cellLevelCharacteristics, int row, double q)
static double[]	sampleStandardDeviation(SingleCellExpressionDataVector vector)
static double	sampleStandardDeviation(SingleCellExpressionDataVector vector, BioAssay sample)
static double[]	sampleVariance(SingleCellExpressionDataVector vector)
static double	sampleVariance(SingleCellExpressionDataVector vector, BioAssay sample)	Calculate the variance of a given assay.
static double[]	sum(SingleCellExpressionDataVector vector)
static double[]	sum(SingleCellExpressionDataVector vector, CellLevelCharacteristics cellLevelCharacteristics)
static double[]	sumUnscaled(SingleCellExpressionDataVector vector)
static double[]	sumWithUnknown(SingleCellExpressionDataVector vector, CellLevelCharacteristics cellLevelCharacteristics)

Methods inherited from class java.lang.Object

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

Constructor Details

SingleCellDescriptive

public SingleCellDescriptive()

Method Details

max

public static double[] max(SingleCellExpressionDataVector vector)

max

public static double max(SingleCellExpressionDataVector vector,
 int sampleIndex)

max

public static double[] max(SingleCellExpressionDataVector vector,
 CellLevelCharacteristics cellLevelCharacteristics)

max

public static double max(SingleCellExpressionDataVector vector,
 int sampleIndex,
 CellLevelCharacteristics cellLevelCharacteristics,
 int row)

min

public static double[] min(SingleCellExpressionDataVector vector)

min

public static double min(SingleCellExpressionDataVector vector,
 int sampleIndex)

min

public static double[] min(SingleCellExpressionDataVector vector,
 CellLevelCharacteristics cellLevelCharacteristics)

min

public static double min(SingleCellExpressionDataVector vector,
 int sampleIndex,
 CellLevelCharacteristics cellLevelCharacteristics,
 int row)

count

public static int[] count(SingleCellExpressionDataVector vector)

Count the number of values in each assay.

Missing values are not counted.

countFast

public static int[] countFast(SingleCellExpressionDataVector vector)

Quickly count the non-zeroes for each assay.

Note: this is not accurate if the single-cell vector contains NaNs or actual zeroes or missing values as per QuantitationTypeUtils.getDefaultCountValueAsDouble(QuantitationType)}.

countFast

public static int countFast(SingleCellExpressionDataVector vector,
 int sampleIndex)

countFast

public static int countFast(SingleCellExpressionDataVector vector,
 int sampleIndex,
 CellLevelCharacteristics cellLevelCharacteristics,
 int row)

countFast

public static int[] countFast(SingleCellExpressionDataVector vector,
 CellLevelCharacteristics cellLevelCharacteristics)

countFastWithUnknown

public static int[] countFastWithUnknown(SingleCellExpressionDataVector vector,
 CellLevelCharacteristics cellLevelCharacteristics)

countAboveThreshold

public static int[] countAboveThreshold(SingleCellExpressionDataVector vector,
 double threshold)

Compute the number of cells expressed strictly above the given threshold.

Parameters:

threshold - a threshold value, assumed to be in the ScaleType of the vector

sum

public static double[] sum(SingleCellExpressionDataVector vector)

sum

public static double[] sum(SingleCellExpressionDataVector vector,
 CellLevelCharacteristics cellLevelCharacteristics)

sumWithUnknown

public static double[] sumWithUnknown(SingleCellExpressionDataVector vector,
 CellLevelCharacteristics cellLevelCharacteristics)

sumUnscaled

public static double[] sumUnscaled(SingleCellExpressionDataVector vector)

mean

public static double[] mean(SingleCellExpressionDataVector vector)

Calculate the mean of each assay for a given vector.

mean

public static double mean(SingleCellExpressionDataVector vector,
 BioAssay sample)

Calculate the mean of a given assay.

mean

public static double mean(SingleCellExpressionDataVector vector,
 int sampleIndex)

mean

public static double mean(SingleCellExpressionDataVector vector,
 int sampleIndex,
 CellLevelCharacteristics cellLevelCharacteristics,
 int row)

median

public static double[] median(SingleCellExpressionDataVector vector)

Calculate the median of each assay for a given vector.

median

public static double median(SingleCellExpressionDataVector vector,
 int column)

median

public static double median(SingleCellExpressionDataVector vector,
 int column,
 CellLevelCharacteristics cellLevelCharacteristics,
 int row)

quantile

public static double[] quantile(SingleCellExpressionDataVector vector,
 double q)

quantile

public static double quantile(SingleCellExpressionDataVector vector,
 int sampleIndex,
 double v)

quantile

public static double[] quantile(SingleCellExpressionDataVector vector,
 CellLevelCharacteristics cellLevelCharacteristics,
 int row,
 double q)

quantile

public static double quantile(SingleCellExpressionDataVector vector,
 int sampleIndex,
 CellLevelCharacteristics cellLevelCharacteristics,
 int row,
 double q)

sampleStandardDeviation

public static double[] sampleStandardDeviation(SingleCellExpressionDataVector vector)

sampleStandardDeviation

public static double sampleStandardDeviation(SingleCellExpressionDataVector vector,
 BioAssay sample)

sampleVariance

public static double[] sampleVariance(SingleCellExpressionDataVector vector)

sampleVariance

public static double sampleVariance(SingleCellExpressionDataVector vector,
 BioAssay sample)

Calculate the variance of a given assay.