Package ubic.gemma.core.datastructure.matrix

Interface ExpressionDataMatrix<T>

Type Parameters:

T - type of scalar held in the matrix

All Known Subinterfaces:

BulkExpressionDataMatrix<T>, BulkExpressionDataPrimitiveDoubleMatrix, BulkExpressionDataPrimitiveIntMatrix, ExpressionDataPrimitiveDoubleMatrix, ExpressionDataPrimitiveIntMatrix, MultiAssayBulkExpressionDataMatrix<T>, SingleCellExpressionDataMatrix<T>

All Known Implementing Classes:

AbstractBulkExpressionDataMatrix, AbstractExpressionDataMatrix, AbstractMultiAssayExpressionDataMatrix, AbstractSingleCellExpressionDataMatrix, BulkExpressionDataDoubleMatrix, BulkExpressionDataIntMatrix, EmptyBulkExpressionDataMatrix, EmptyExpressionMatrix, EmptySingleCellExpressionDataMatrix, ExpressionDataBooleanMatrix, ExpressionDataDoubleMatrix, ExpressionDataIntegerMatrix, ExpressionDataStringMatrix, MaskedExpressionDataMatrix, SingleCellExpressionDataDoubleMatrix, SingleCellExpressionDataIntMatrix

public interface ExpressionDataMatrix<T>

Represents a matrix of data from an ExpressionExperiment.

The rows of this matrix represent design elements.

Author:

pavlidis, keshav

See Also:

• BulkExpressionDataMatrix
• SingleCellExpressionDataMatrix

Method Summary

Modifier and Type	Method	Description
int	columns()	Obtain the total number of columns.
T	get(int row, int column)	Access a single value of the matrix by row and column.
T[]	getColumn(int column)	Access a single column of the matrix.
CompositeSequence	getDesignElementForRow(int index)	Return a design element for a given index.
List<CompositeSequence>	getDesignElements()	Obtain all the design elements in this data matrix.
ExpressionExperiment	getExpressionExperiment()	Return the expression experiment this matrix is holding data for, if known.
QuantitationType	getQuantitationType()	Obtain the quantitation type for this matrix.
T[]	getRow(int index)	Access a single row of the matrix, by index.
T[]	getRow(CompositeSequence designElement)	Return a row that 'came from' the given design element.
ExpressionDataMatrixRowElement	getRowElement(int row)	Deprecated. use getDesignElementForRow(int) instead
List<ExpressionDataMatrixRowElement>	getRowElements()	Deprecated. use getDesignElements() instead
int	getRowIndex(CompositeSequence designElement)
int[]	getRowIndices(CompositeSequence designElement)	Obtain all the rows that correspond to the given design element, or null if the design element is not found.
int	rows()
ExpressionDataMatrix<T>	sliceRows(List<CompositeSequence> designElements)

Method Details

getExpressionExperiment

@Nullable
ExpressionExperiment getExpressionExperiment()

Return the expression experiment this matrix is holding data for, if known.

getQuantitationType

QuantitationType getQuantitationType()

Obtain the quantitation type for this matrix.

getDesignElements

List<CompositeSequence> getDesignElements()

Obtain all the design elements in this data matrix.

getDesignElementForRow

CompositeSequence getDesignElementForRow(int index)

Return a design element for a given index.

Throws:

IndexOutOfBoundsException - if the supplied index is not within zero and rows()

columns

int columns()

Obtain the total number of columns.

getColumn

T[] getColumn(int column)

Access a single column of the matrix.

Parameters:

column - index

Returns:

T[]

Throws:

IndexOutOfBoundsException - if the supplied index is not within zero and columns()

rows

int rows()

Returns:

int

getRow

T[] getRow(int index)

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

Parameters:

index - i

Returns:

t[]

Throws:

IndexOutOfBoundsException - if the supplied index is not within zero and rows()

getRow

@Nullable
T[] getRow(CompositeSequence designElement)

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

Parameters:

designElement - de

Returns:

the corresponding row or null if the design element is not found in the matrix

getRowIndex

int getRowIndex(CompositeSequence designElement)

Returns:

the index for the given design element, or -1 if not found

getRowIndices

@Nullable
int[] getRowIndices(CompositeSequence designElement)

Obtain all the rows that correspond to the given design element, or null if the design element is not found.

sliceRows

ExpressionDataMatrix<T> sliceRows(List<CompositeSequence> designElements)

getRowElements

@Deprecated
List<ExpressionDataMatrixRowElement> getRowElements()

Deprecated.

use getDesignElements() instead

Returns:

list of elements representing the row 'labels'.

getRowElement

@Deprecated
ExpressionDataMatrixRowElement getRowElement(int row)

Deprecated.

use getDesignElementForRow(int) instead

Throws:

IndexOutOfBoundsException - if the supplied index is not within zero and rows()

get

T get(int row,
 int column)

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

Throws:

IndexOutOfBoundsException - if either the row or column is outside the matrix bounds