Package ubic.gemma.core.datastructure.matrix

Class ExpressionDataDoubleMatrix

java.lang.Object

ubic.gemma.core.datastructure.matrix.AbstractExpressionDataMatrix<Double>

ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix<Double>

ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix

All Implemented Interfaces:

BulkExpressionDataMatrix<Double>, BulkExpressionDataPrimitiveDoubleMatrix, ExpressionDataMatrix<Double>, ExpressionDataPrimitiveDoubleMatrix, MultiAssayBulkExpressionDataMatrix<Double>, SingleCellDerivedBulkExpressionDataMatrix<Double>

public class ExpressionDataDoubleMatrix
extends AbstractMultiAssayExpressionDataMatrix<Double>
implements BulkExpressionDataPrimitiveDoubleMatrix, SingleCellDerivedBulkExpressionDataMatrix<Double>

A data structure that holds a reference to the data for a given expression experiment. The data can be queried by row or column, returning data for a specific DesignElement or data for a specific BioAssay. This class is not database aware so the vectors provided must already be 'thawed'.

Author:

pavlidis, keshav

Constructor Summary

Constructors

Constructor	Description
ExpressionDataDoubleMatrix(ExpressionDataDoubleMatrix sourceMatrix, int[][] numberOfCells)
ExpressionDataDoubleMatrix(ExpressionExperiment ee, Collection<? extends BulkExpressionDataVector> vectors)
ExpressionDataDoubleMatrix(ExpressionExperiment ee, Collection<? extends BulkExpressionDataVector> dataVectors, Collection<QuantitationType> quantitationTypes)
ExpressionDataDoubleMatrix(ExpressionExperiment ee, Collection<? extends BulkExpressionDataVector> dataVectors, QuantitationType quantitationType)
ExpressionDataDoubleMatrix(ExpressionExperiment ee, DoubleMatrix<CompositeSequence,BioMaterial> dataMatrix, QuantitationType qt)	Create a matrix given a 'raw' matrix that uses the same samples as the experiment.

Method Summary

Modifier and Type	Method	Description
protected String	format(int row, int column)	Format the value at the provided indices of the matrix.
Double	get(int row, int column)	Access a single value of the matrix by row and column.
double	getAsDouble(int row, int column)	Retrieve the value at the given row and column without boxing.
Double[]	getColumn(int index)	Access a single column of the matrix.
double[]	getColumnAsDoubles(int index)	Retrieve the given column without boxing.
double[]	getColumnAsDoubles(BioAssay bioAssay)	Retrieve the given column without boxing.
DoubleMatrix<CompositeSequence,BioMaterial>	getMatrix()
int[][]	getNumberOfCells()
Integer	getNumberOfCells(int row, int column)
int[]	getNumberOfCellsForColumn(int column)
int[]	getNumberOfCellsForColumn(BioMaterial bioMaterial)
int[]	getNumberOfCellsForRow(int row)
int[]	getNumberOfCellsForRow(CompositeSequence designElement)
Map<CompositeSequence,Double>	getRanksByMean()
Double[][]	getRawMatrix()	Access the entire matrix.
double[][]	getRawMatrixAsDoubles()	Obtain the raw matrix without boxing.
Double[]	getRow(int index)	Access a single row of the matrix, by index.
double[]	getRowAsDoubles(int index)	Retrieve a row without boxing.
double[]	getRowAsDoubles(CompositeSequence designElement)	Retrieve the row for the given design element without boxing.
List<CompositeSequence>	getRowNames()
boolean	hasMissingValues()
void	set(int row, int column, Double value)	Deprecated. modifying the matrix directly is not recommended, make a copy instead.
void	set(CompositeSequence designElement, BioAssay bioAssay, Double value)	Deprecated.
ExpressionDataDoubleMatrix	sliceColumns(List<BioMaterial> bioMaterials)	Slice the requested samples (columns) from this matrix.
ExpressionDataDoubleMatrix	sliceColumns(List<BioMaterial> bioMaterials, BioAssayDimension reorderedDim)	Slice the requested samples (columns) from this matrix.
ExpressionDataDoubleMatrix	sliceRows(List<CompositeSequence> designElements)	Slice the given design elements (rows) from the matrix.
ExpressionDataDoubleMatrix	withMatrix(DoubleMatrix<CompositeSequence,BioMaterial> matrix)	Create a copy of this matrix with the given data matrix.
ExpressionDataDoubleMatrix	withMatrix(DoubleMatrix<CompositeSequence,BioMaterial> matrix, Map<QuantitationType,QuantitationType> quantitationTypes)	Create a copy of this matrix with the given data matrix and quantitation types.
ExpressionDataDoubleMatrix	withNumberOfCells(int[][] numberOfCells)

Methods inherited from class ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix

addToRowMaps, addToRowMaps, columns, columns, formatRepresentation, get, getBestBioAssayDimension, getBioAssayDimension, getBioAssayDimension, getBioAssayDimensions, getBioAssayForColumn, getBioAssaysForColumn, getBioMaterialForColumn, getBioMaterials, getColumn, getColumnIndex, getColumnIndex, getColumnLabel, getDesignElementForRow, getDesignElements, getExpressionExperiment, getQuantitationType, getQuantitationType, getQuantitationTypes, getRow, getRowElement, getRowElements, getRowIndex, getRowIndices, getRowLabel, rows, selectVectors, selectVectors, selectVectors, selectVectors, setUpColumnElements, setUpColumnElements

Methods inherited from class ubic.gemma.core.datastructure.matrix.AbstractExpressionDataMatrix

format, format, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface ubic.gemma.core.datastructure.matrix.BulkExpressionDataMatrix

get, getBioAssayForColumn, getBioMaterials, getColumn, getColumnIndex

Methods inherited from interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix

columns, getDesignElementForRow, getDesignElements, getExpressionExperiment, getRow, getRowElement, getRowElements, getRowIndex, getRowIndices, rows

Constructor Details

ExpressionDataDoubleMatrix

public ExpressionDataDoubleMatrix(@Nullable
 ExpressionExperiment ee,
 Collection<? extends BulkExpressionDataVector> vectors)

ExpressionDataDoubleMatrix

public ExpressionDataDoubleMatrix(ExpressionExperiment ee,
 Collection<? extends BulkExpressionDataVector> dataVectors,
 Collection<QuantitationType> quantitationTypes)

ExpressionDataDoubleMatrix

public ExpressionDataDoubleMatrix(ExpressionExperiment ee,
 Collection<? extends BulkExpressionDataVector> dataVectors,
 QuantitationType quantitationType)

ExpressionDataDoubleMatrix

public ExpressionDataDoubleMatrix(ExpressionExperiment ee,
 DoubleMatrix<CompositeSequence,BioMaterial> dataMatrix,
 QuantitationType qt)

Create a matrix given a 'raw' matrix that uses the same samples as the experiment. Only simple situations are supported (one platform, not subsetting the dataset).

Parameters:

ee - to be associated with this

dataMatrix - with valid row and column elements, and the data

qt - to be associated with this

ExpressionDataDoubleMatrix

public ExpressionDataDoubleMatrix(ExpressionDataDoubleMatrix sourceMatrix,
 @Nullable
 int[][] numberOfCells)

Method Details

get

public Double get(int row,
 int column)

Description copied from interface: ExpressionDataMatrix

Access a single value of the matrix by row and column.

Specified by:

get in interface ExpressionDataMatrix<Double>

getAsDouble

public double getAsDouble(int row,
 int column)

Description copied from interface: ExpressionDataPrimitiveDoubleMatrix

Retrieve the value at the given row and column without boxing.

Specified by:

getAsDouble in interface ExpressionDataPrimitiveDoubleMatrix

See Also:

• ExpressionDataMatrix.get(int, int)

getColumnAsDoubles

public double[] getColumnAsDoubles(BioAssay bioAssay)

Description copied from interface: BulkExpressionDataPrimitiveDoubleMatrix

Retrieve the given column without boxing.

Specified by:

getColumnAsDoubles in interface BulkExpressionDataPrimitiveDoubleMatrix

See Also:

• BulkExpressionDataMatrix.getColumn(BioAssay)

getColumn

public Double[] getColumn(int index)

Description copied from interface: ExpressionDataMatrix

Access a single column of the matrix.

Specified by:

getColumn in interface ExpressionDataMatrix<Double>

Parameters:

index - index

Returns:

T[]

getColumnAsDoubles

public double[] getColumnAsDoubles(int index)

Description copied from interface: ExpressionDataPrimitiveDoubleMatrix

Retrieve the given column without boxing.

Specified by:

getColumnAsDoubles in interface ExpressionDataPrimitiveDoubleMatrix

See Also:

• ExpressionDataMatrix.getColumn(int)

sliceColumns

public ExpressionDataDoubleMatrix sliceColumns(List<BioMaterial> bioMaterials)

Description copied from interface: BulkExpressionDataMatrix

Slice the requested samples (columns) from this matrix.

Dimensions will be altered to reflect only the selected samples.

Specified by:

sliceColumns in interface BulkExpressionDataMatrix<Double>

Parameters:

bioMaterials - samples to select from the matrix

sliceColumns

public ExpressionDataDoubleMatrix sliceColumns(List<BioMaterial> bioMaterials,
 BioAssayDimension reorderedDim)

Description copied from interface: BulkExpressionDataMatrix

Slice the requested samples (columns) from this matrix.

This also allows specifying a new dimension for the columns that will be used for every design element (rows).

Specified by:

sliceColumns in interface BulkExpressionDataMatrix<Double>

Parameters:

bioMaterials - samples to select from the matrix

reorderedDim - the dimension to use

getRawMatrix

public Double[][] getRawMatrix()

Description copied from interface: BulkExpressionDataMatrix

Access the entire matrix.

Specified by:

getRawMatrix in interface BulkExpressionDataMatrix<Double>

Returns:

T[][]

getRawMatrixAsDoubles

public double[][] getRawMatrixAsDoubles()

Obtain the raw matrix without boxing.

Specified by:

getRawMatrixAsDoubles in interface BulkExpressionDataPrimitiveDoubleMatrix

See Also:

• getRawMatrix()

getRowAsDoubles

public double[] getRowAsDoubles(CompositeSequence designElement)

Description copied from interface: ExpressionDataPrimitiveDoubleMatrix

Retrieve the row for the given design element without boxing.

Specified by:

getRowAsDoubles in interface ExpressionDataPrimitiveDoubleMatrix

See Also:

• ExpressionDataMatrix.getRow(CompositeSequence)

getRow

public Double[] getRow(int index)

Description copied from interface: ExpressionDataMatrix

Access a single row of the matrix, by index. A complete row is returned.

Specified by:

getRow in interface ExpressionDataMatrix<Double>

Parameters:

index - i

Returns:

t[]

sliceRows

public ExpressionDataDoubleMatrix sliceRows(List<CompositeSequence> designElements)

Description copied from interface: ExpressionDataMatrix

Slice the given design elements (rows) from the matrix.

Specified by:

sliceRows in interface ExpressionDataMatrix<Double>

getRowAsDoubles

public double[] getRowAsDoubles(int index)

Description copied from interface: ExpressionDataPrimitiveDoubleMatrix

Retrieve a row without boxing.

Specified by:

getRowAsDoubles in interface ExpressionDataPrimitiveDoubleMatrix

See Also:

• ExpressionDataMatrix.getRow(int)

hasMissingValues

public boolean hasMissingValues()

Specified by:

hasMissingValues in interface BulkExpressionDataMatrix<Double>

Returns:

true if any values are null or NaN (for doubles and floats); any other value that is considered missing.

set

@Deprecated
public void set(int row,
 int column,
 @Nullable
 Double value)

Deprecated.

modifying the matrix directly is not recommended, make a copy instead.

getMatrix

public DoubleMatrix<CompositeSequence,BioMaterial> getMatrix()

withMatrix

public ExpressionDataDoubleMatrix withMatrix(DoubleMatrix<CompositeSequence,BioMaterial> matrix)

Create a copy of this matrix with the given data matrix.

withMatrix

public ExpressionDataDoubleMatrix withMatrix(DoubleMatrix<CompositeSequence,BioMaterial> matrix,
 Map<QuantitationType,QuantitationType> quantitationTypes)

Create a copy of this matrix with the given data matrix and quantitation types.

Use this if the matrix and quantitation types are both changing (i.e. normalizing resulting in the flag to be altered

getNumberOfCells

@Nullable
public int[][] getNumberOfCells()

Specified by:

getNumberOfCells in interface SingleCellDerivedBulkExpressionDataMatrix<Double>

getNumberOfCells

@Nullable
public Integer getNumberOfCells(int row,
 int column)

Specified by:

getNumberOfCells in interface SingleCellDerivedBulkExpressionDataMatrix<Double>

getNumberOfCellsForColumn

@Nullable
public int[] getNumberOfCellsForColumn(int column)

Specified by:

getNumberOfCellsForColumn in interface SingleCellDerivedBulkExpressionDataMatrix<Double>

getNumberOfCellsForColumn

@Nullable
public int[] getNumberOfCellsForColumn(BioMaterial bioMaterial)

Specified by:

getNumberOfCellsForColumn in interface SingleCellDerivedBulkExpressionDataMatrix<Double>

getNumberOfCellsForRow

@Nullable
public int[] getNumberOfCellsForRow(int row)

Specified by:

getNumberOfCellsForRow in interface SingleCellDerivedBulkExpressionDataMatrix<Double>

getNumberOfCellsForRow

@Nullable
public int[] getNumberOfCellsForRow(CompositeSequence designElement)

Specified by:

getNumberOfCellsForRow in interface SingleCellDerivedBulkExpressionDataMatrix<Double>

withNumberOfCells

public ExpressionDataDoubleMatrix withNumberOfCells(@Nullable
 int[][] numberOfCells)

getRanksByMean

public Map<CompositeSequence,Double> getRanksByMean()

Returns:

The expression level ranks (based on mean signal intensity in the vectors)

getRowNames

public List<CompositeSequence> getRowNames()

set

@Deprecated
public void set(CompositeSequence designElement,
 BioAssay bioAssay,
 Double value)

Deprecated.

format

protected String format(int row,
 int column)

Description copied from class: AbstractMultiAssayExpressionDataMatrix

Format the value at the provided indices of the matrix.

Specified by:

format in class AbstractMultiAssayExpressionDataMatrix<Double>