Package ubic.gemma.persistence.service.expression.bioAssayData

Class RandomSingleCellDataUtils

java.lang.Object

ubic.gemma.persistence.service.expression.bioAssayData.RandomSingleCellDataUtils

public class RandomSingleCellDataUtils
extends Object

Utilities for generating random single-cell data.

Author:

poirigui

See Also:

RandomExpressionDataMatrixUtils, RandomBulkDataUtils

Constructor Summary

Constructors

Constructor	Description
RandomSingleCellDataUtils()

Method Summary

Modifier and Type	Method	Description
static ubic.gemma.model.expression.bioAssayData.CellTypeAssignment	randomCellTypeAssignment(ubic.gemma.model.expression.bioAssayData.SingleCellDimension scd)	Generate a random cell type assignment with 10 cell types and 10% sparsity.
static ubic.gemma.model.expression.bioAssayData.CellTypeAssignment	randomCellTypeAssignment(ubic.gemma.model.expression.bioAssayData.SingleCellDimension scd, int numberOfCellTypes, double sparsity)
static ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVector	randomSingleCellVector(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, ubic.gemma.model.expression.designElement.CompositeSequence compositeSequence, ubic.gemma.model.common.quantitationtype.QuantitationType qt, int numCellsPerBioAssay, double sparsity)
static ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVector	randomSingleCellVector(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, ubic.gemma.model.expression.designElement.CompositeSequence compositeSequence, ubic.gemma.model.common.quantitationtype.QuantitationType qt, ubic.gemma.model.expression.bioAssayData.SingleCellDimension dimension, double sparsity)	Generate a single random single-cell vector.
static List<ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVector>	randomSingleCellVectors()
static List<ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVector>	randomSingleCellVectors(int numDesignElements, int numSamples, int numCellsPerBioAssay, double sparsity, ubic.gemma.model.common.quantitationtype.ScaleType scaleType)
static List<ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVector>	randomSingleCellVectors(ubic.gemma.model.common.quantitationtype.QuantitationType quantitationType)
static List<ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVector>	randomSingleCellVectors(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, ubic.gemma.model.expression.arrayDesign.ArrayDesign ad, ubic.gemma.model.common.quantitationtype.QuantitationType qt)	Generate random single-cell vectors with 1000 cells/sample and 90% sparsity.
static List<ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVector>	randomSingleCellVectors(ubic.gemma.model.expression.experiment.ExpressionExperiment ee, ubic.gemma.model.expression.arrayDesign.ArrayDesign ad, ubic.gemma.model.common.quantitationtype.QuantitationType qt, int numCellsPerBioAssay, double sparsity)	Generate random single-cell vectors.
static void	setSeed(long seed)	Set the seed used to generate random single-cell vectors.

Methods inherited from class java.lang.Object

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

Constructor Detail

RandomSingleCellDataUtils

public RandomSingleCellDataUtils()

Method Detail

setSeed

public static void setSeed(long seed)

Set the seed used to generate random single-cell vectors.

randomSingleCellVectors

public static List<ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVector> randomSingleCellVectors()

randomSingleCellVectors

public static List<ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVector> randomSingleCellVectors(ubic.gemma.model.common.quantitationtype.QuantitationType quantitationType)

randomSingleCellVectors

public static List<ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVector> randomSingleCellVectors(int numDesignElements,
                                                                                                                    int numSamples,
                                                                                                                    int numCellsPerBioAssay,
                                                                                                                    double sparsity,
                                                                                                                    ubic.gemma.model.common.quantitationtype.ScaleType scaleType)

randomSingleCellVectors

public static List<ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVector> randomSingleCellVectors(ubic.gemma.model.expression.experiment.ExpressionExperiment ee,
                                                                                                                    ubic.gemma.model.expression.arrayDesign.ArrayDesign ad,
                                                                                                                    ubic.gemma.model.common.quantitationtype.QuantitationType qt)

Generate random single-cell vectors with 1000 cells/sample and 90% sparsity.

See Also:

randomSingleCellVectors(ExpressionExperiment, ArrayDesign, QuantitationType, int, double)

randomSingleCellVectors

public static List<ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVector> randomSingleCellVectors(ubic.gemma.model.expression.experiment.ExpressionExperiment ee,
                                                                                                                    ubic.gemma.model.expression.arrayDesign.ArrayDesign ad,
                                                                                                                    ubic.gemma.model.common.quantitationtype.QuantitationType qt,
                                                                                                                    int numCellsPerBioAssay,
                                                                                                                    double sparsity)

Generate random single-cell vectors.

Counts are drawn from a NegativeBinomial.

One vector is generated by design element from the provided array design with the given sparsity.

Parameters:

numCellsPerBioAssay - how many cells to generate per BioAssay

sparsity - sparsity of the vectors

randomSingleCellVector

public static ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVector randomSingleCellVector(ubic.gemma.model.expression.experiment.ExpressionExperiment ee,
                                                                                                             ubic.gemma.model.expression.designElement.CompositeSequence compositeSequence,
                                                                                                             ubic.gemma.model.common.quantitationtype.QuantitationType qt,
                                                                                                             int numCellsPerBioAssay,
                                                                                                             double sparsity)

randomSingleCellVector

public static ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVector randomSingleCellVector(ubic.gemma.model.expression.experiment.ExpressionExperiment ee,
                                                                                                             ubic.gemma.model.expression.designElement.CompositeSequence compositeSequence,
                                                                                                             ubic.gemma.model.common.quantitationtype.QuantitationType qt,
                                                                                                             ubic.gemma.model.expression.bioAssayData.SingleCellDimension dimension,
                                                                                                             double sparsity)

Generate a single random single-cell vector.

randomCellTypeAssignment

public static ubic.gemma.model.expression.bioAssayData.CellTypeAssignment randomCellTypeAssignment(ubic.gemma.model.expression.bioAssayData.SingleCellDimension scd)

Generate a random cell type assignment with 10 cell types and 10% sparsity.

randomCellTypeAssignment

public static ubic.gemma.model.expression.bioAssayData.CellTypeAssignment randomCellTypeAssignment(ubic.gemma.model.expression.bioAssayData.SingleCellDimension scd,
                                                                                                   int numberOfCellTypes,
                                                                                                   double sparsity)