Interface ExpressionDataMatrix<T>

Type Parameters:
T - type of scalar held in the matrix
All Known Subinterfaces:
BulkExpressionDataMatrix<T>, BulkExpressionDataPrimitiveDoubleMatrix, BulkExpressionDataPrimitiveIntMatrix, ExpressionDataPrimitiveDoubleMatrix, ExpressionDataPrimitiveIntMatrix, MultiAssayBulkExpressionDataMatrix<T>, SingleCellDerivedBulkExpressionDataMatrix<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:

  • 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)
      Slice the given design elements (rows) from the matrix.
      Throws:
      IllegalArgumentException - if any of the requested design element is not present in the matrix

    • 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