Package ubic.gemma.core.datastructure.matrix

Class ExpressionDataDoubleMatrix

java.lang.Object

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

ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix

All Implemented Interfaces:

Serializable, ExpressionDataMatrix<Double>

public class ExpressionDataDoubleMatrix
extends BaseExpressionDataMatrix<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

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
ExpressionDataDoubleMatrix()	To comply with bean specifications.
ExpressionDataDoubleMatrix(Collection<? extends DesignElementDataVector> vectors)
ExpressionDataDoubleMatrix(Collection<? extends DesignElementDataVector> dataVectors, Collection<QuantitationType> quantitationTypes)
ExpressionDataDoubleMatrix(Collection<? extends DesignElementDataVector> dataVectors, QuantitationType quantitationType)
ExpressionDataDoubleMatrix(ExpressionDataDoubleMatrix sourceMatrix, List<BioMaterial> columnsToUse, BioAssayDimension reorderedDim)	Create a matrix based on another one's selected columns.
ExpressionDataDoubleMatrix(ExpressionDataDoubleMatrix sourceMatrix, List<CompositeSequence> rowsToUse)	Create a matrix based on another one's selected rows.
ExpressionDataDoubleMatrix(ExpressionDataDoubleMatrix sourceMatrix, DoubleMatrix<CompositeSequence,BioMaterial> dataMatrix, Collection<QuantitationType> quantitationTypes)	Create a data matrix like sourceMatrix but use the values and quantitations from dataMatrix.
ExpressionDataDoubleMatrix(ExpressionExperiment ee, QuantitationType qt, DoubleMatrix<CompositeSequence,BioMaterial> matrix)	Create a matrix given a 'raw' matrix that uses the same samples as the experiment.

Method Summary

Modifier and Type	Method	Description
int	columns()	Total number of columns.
Double	get(int row, int column)	Access a single value of the matrix.
Double[][]	get(List<CompositeSequence> designElements, List<BioAssay> bioAssays)	Access a submatrix
Double	get(CompositeSequence designElement, BioAssay bioAssay)	Access a single value of the matrix.
Double[]	getColumn(Integer index)	Access a single column of the matrix.
Double[]	getColumn(BioAssay bioAssay)	Access a single column of the matrix.
Double[][]	getColumns(List<BioAssay> bioAssays)	Access a submatrix slice by columns
DoubleMatrix<CompositeSequence,BioMaterial>	getMatrix()
Map<CompositeSequence,Double>	getRanks()
Double[][]	getRawMatrix()	Access the entire matrix.
double[]	getRawRow(Integer index)
Double[]	getRow(Integer index)	Access a single row of the matrix, by index.
Double[]	getRow(CompositeSequence designElement)	Return a row that 'came from' the given design element.
List<CompositeSequence>	getRowNames()
Double[][]	getRows(List<CompositeSequence> designElements)	Access a submatrix
boolean	hasMissingValues()
int	rows()
void	set(int row, int column, Double value)	Set a value in the matrix, by index
void	set(CompositeSequence designElement, BioAssay bioAssay, Double value)
void	setRow(int rowIndex, Double[] data)	Sets the row of matrix to the input data.
Collection<ProcessedExpressionDataVector>	toProcessedDataVectors()
Collection<RawExpressionDataVector>	toRawDataVectors()	Same as toProcessedDataVectors but uses RawExpressionDataVector
String	toString()
protected void	vectorsToMatrix(Collection<? extends DesignElementDataVector> vectors)	Convert DesignElementDataVectors into Double matrix.

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

columns, getBestBioAssayDimension, getBioAssayDimension, getBioAssaysForColumn, getBioMaterialForColumn, getColumnIndex, getDesignElementForRow, getDesignElements, getExpressionExperiment, getQuantitationTypes, getRowElement, getRowElements, getRowIndex

Methods inherited from class java.lang.Object

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

Constructor Detail

ExpressionDataDoubleMatrix

public ExpressionDataDoubleMatrix()

To comply with bean specifications. Not to be instantiated.

ExpressionDataDoubleMatrix

public ExpressionDataDoubleMatrix(Collection<? extends DesignElementDataVector> vectors)

ExpressionDataDoubleMatrix

public ExpressionDataDoubleMatrix(Collection<? extends DesignElementDataVector> dataVectors,
                                  Collection<QuantitationType> quantitationTypes)

ExpressionDataDoubleMatrix

public ExpressionDataDoubleMatrix(Collection<? extends DesignElementDataVector> dataVectors,
                                  QuantitationType quantitationType)

ExpressionDataDoubleMatrix

public ExpressionDataDoubleMatrix(ExpressionDataDoubleMatrix sourceMatrix,
                                  DoubleMatrix<CompositeSequence,BioMaterial> dataMatrix,
                                  Collection<QuantitationType> quantitationTypes)

Create a data matrix like sourceMatrix but use the values and quantitations from dataMatrix.

Note: The rows can be different from the original matrix, but the columns must be the same.

Parameters:

sourceMatrix - source matrix from which most of the meta-data will be imported

dataMatrix - data matrix to use

quantitationTypes - quantitation types used by the dataMatrix

ExpressionDataDoubleMatrix

public ExpressionDataDoubleMatrix(ExpressionDataDoubleMatrix sourceMatrix,
                                  List<CompositeSequence> rowsToUse)

Create a matrix based on another one's selected rows.

Parameters:

rowsToUse - rows

sourceMatrix - matrix

ExpressionDataDoubleMatrix

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

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

qt - to be associated with this

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

ExpressionDataDoubleMatrix

public ExpressionDataDoubleMatrix(ExpressionDataDoubleMatrix sourceMatrix,
                                  List<BioMaterial> columnsToUse,
                                  BioAssayDimension reorderedDim)

Create a matrix based on another one's selected columns. The results will be somewhat butchered - only a single BioAssayDimension and the ranks will be copied over (not recomputed based on the selected columns).

Parameters:

columnsToUse - columns

sourceMatrix - matrix

reorderedDim - the reordered bioAssayDimension.

Method Detail

columns

public int columns()

Description copied from interface: ExpressionDataMatrix

Total number of columns.

Returns:

int

get

public Double get(CompositeSequence designElement,
                  BioAssay bioAssay)

Description copied from interface: ExpressionDataMatrix

Access a single value of the matrix. Note that because there can be multiple bioassays per column and multiple designelements per row, it is possible for this method to retrieve a data that does not come from the bioassay and/or designelement arguments.

Parameters:

designElement - de

bioAssay - ba

Returns:

T t

get

public Double get(int row,
                  int column)

Description copied from interface: ExpressionDataMatrix

Access a single value of the matrix. This is generally the easiest way to do it.

Parameters:

row - row

column - col

Returns:

t

get

public Double[][] get(List<CompositeSequence> designElements,
                      List<BioAssay> bioAssays)

Description copied from interface: ExpressionDataMatrix

Access a submatrix

Parameters:

designElements - de

bioAssays - bas

Returns:

T[][]

getColumn

public Double[] getColumn(BioAssay bioAssay)

Description copied from interface: ExpressionDataMatrix

Access a single column of the matrix.

Parameters:

bioAssay - i

Returns:

T[]

getColumn

public Double[] getColumn(Integer index)

Description copied from interface: ExpressionDataMatrix

Access a single column of the matrix.

Parameters:

index - index

Returns:

T[]

getColumns

public Double[][] getColumns(List<BioAssay> bioAssays)

Description copied from interface: ExpressionDataMatrix

Access a submatrix slice by columns

Parameters:

bioAssays - ba

Returns:

t[][]

getRawMatrix

public Double[][] getRawMatrix()

Description copied from interface: ExpressionDataMatrix

Access the entire matrix.

Returns:

T[][]

getRow

public Double[] getRow(CompositeSequence designElement)

Description copied from interface: ExpressionDataMatrix

Return a row that 'came from' the given design element.

Parameters:

designElement - de

Returns:

t

getRow

public Double[] getRow(Integer index)

Description copied from interface: ExpressionDataMatrix

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

Parameters:

index - i

Returns:

t[]

getRows

public Double[][] getRows(List<CompositeSequence> designElements)

Description copied from interface: ExpressionDataMatrix

Access a submatrix

Parameters:

designElements - de

Returns:

T[][]

hasMissingValues

public boolean hasMissingValues()

Returns:

true if any values are null or NaN (for Doubles); all other values are considered non-missing.

rows

public int rows()

Returns:

int

set

public void set(int row,
                int column,
                Double value)

Description copied from interface: ExpressionDataMatrix

Set a value in the matrix, by index

Parameters:

row - row

column - col

value - val

toProcessedDataVectors

public Collection<ProcessedExpressionDataVector> toProcessedDataVectors()

Returns:

Convert this to a collection of vectors.

toRawDataVectors

public Collection<RawExpressionDataVector> toRawDataVectors()

Same as toProcessedDataVectors but uses RawExpressionDataVector

Returns:

Convert this to a collection of vectors.

getMatrix

public DoubleMatrix<CompositeSequence,BioMaterial> getMatrix()

getRanks

public Map<CompositeSequence,Double> getRanks()

Returns:

The expression level ranks (based on mean signal intensity in the vectors); this will be empty if the vectors used to construct the matrix were not ProcessedExpressionDataVectors.

getRawRow

public double[] getRawRow(Integer index)

getRowNames

public List<CompositeSequence> getRowNames()

set

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

setRow

public void setRow(int rowIndex,
                   Double[] data)

Sets the row of matrix to the input data.

Parameters:

rowIndex - The row index of the data in the matrix to be replaced.

data - The input data.

toString

public String toString()

Overrides:

toString in class Object

vectorsToMatrix

protected void vectorsToMatrix(Collection<? extends DesignElementDataVector> vectors)

Convert DesignElementDataVectors into Double matrix.

Specified by:

vectorsToMatrix in class BaseExpressionDataMatrix<Double>