Package ubic.gemma.core.datastructure.matrix

Interface SingleCellExpressionDataMatrix<T>

All Superinterfaces:
ExpressionDataMatrix<T>
All Known Implementing Classes:
AbstractSingleCellExpressionDataMatrix, EmptySingleCellExpressionDataMatrix, SingleCellExpressionDataDoubleMatrix, SingleCellExpressionDataIntMatrix
public interface SingleCellExpressionDataMatrix<T> extends ExpressionDataMatrix<T>
In a single-cell expression data matrix, each column represents a cell.

Note that the matrix implementation does not deal with all the complication that you may encounter in MultiAssayBulkExpressionDataMatrix. For example, a single-cell data matrix may only hold vectors from one given quantitation type and single-cell dimension at a time.

Author:
poirigui

  • Method Details

    • getMatrix

      static SingleCellExpressionDataMatrix<?> getMatrix(List<SingleCellExpressionDataVector> vectors)

    • getQuantitationType

      QuantitationType getQuantitationType()
      Return the quantitation type for this matrix.
      Specified by:
      getQuantitationType in interface ExpressionDataMatrix<T>

    • getSingleCellDimension

      SingleCellDimension getSingleCellDimension()
      Return the single-cell dimension for this matrix.

    • getColumn

      T[] getColumn(int column)
      Access a single column of the matrix.

      Important note: Retrieving a column is a O(n log m) operation where n is the number of vectors and m is the number of cells. Always favour row-oriented operations when possible.

      Specified by:
      getColumn in interface ExpressionDataMatrix<T>
      Parameters:
      column - index
      Returns:
      T[]

    • getBioAssays

      List<BioAssay> getBioAssays()
      Obtain the list of bioassays.

    • getBioAssayForColumn

      BioAssay getBioAssayForColumn(int j)
      Obtain a bioassay applicable to a given column.

    • getBioMaterialForColumn

      BioMaterial getBioMaterialForColumn(int j)

    • getCellIds

      List<String> getCellIds()
      Note: cell IDs are only unique within a given assay

    • getCellIdForColumn

      String getCellIdForColumn(int j)
      Obtain the cell ID of a given column.