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 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)

Methods inherited from class java.lang.Object

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

Constructor Detail

SingleCellDescriptive

public SingleCellDescriptive()

Method Detail

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 DataVectorDescriptive.getMissingCountValue(QuantitationType)}.

countFast

public static int countFast(SingleCellExpressionDataVector vector,
                            int sampleIndex)

countFast

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

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)

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.