Uses of Class
ubic.basecode.dataStructure.matrix.DoubleMatrix

Packages that use DoubleMatrix

Package	Description
ubic.basecode.datafilter
ubic.basecode.dataStructure
ubic.basecode.dataStructure.matrix
ubic.basecode.graphics
ubic.basecode.io.reader
ubic.basecode.math
ubic.basecode.math.linalg
ubic.basecode.math.linearmodels
ubic.basecode.util
ubic.basecode.util.r

Uses of DoubleMatrix in ubic.basecode.datafilter

Methods in ubic.basecode.datafilter that return DoubleMatrix

Modifier and Type	Method and Description
DoubleMatrix<R,C>	RowLevelFilter.filter(DoubleMatrix<R,C> data)
DoubleMatrix<R,C>	ItemLevelFilter.filter(DoubleMatrix<R,C> data)

Methods in ubic.basecode.datafilter with parameters of type DoubleMatrix

Modifier and Type	Method and Description
DoubleMatrix<R,C>	RowLevelFilter.filter(DoubleMatrix<R,C> data)
DoubleMatrix<R,C>	ItemLevelFilter.filter(DoubleMatrix<R,C> data)

Uses of DoubleMatrix in ubic.basecode.dataStructure

Methods in ubic.basecode.dataStructure that return DoubleMatrix

Modifier and Type	Method and Description
static DoubleMatrix<String,String>	StringToStringSetMap.setMapToMatrix(StringToStringSetMap input)

Uses of DoubleMatrix in ubic.basecode.dataStructure.matrix

Subclasses of DoubleMatrix in ubic.basecode.dataStructure.matrix

Modifier and Type	Class and Description
class	CompressedSparseDoubleMatrix<R,C> Supports sparse matrices (where sparse means most values are zero, not that they are missing).
class	DenseDoubleMatrix<R,C> A dense matrix of doubles that knows about row and column names.
class	FastRowAccessDoubleMatrix<R,C> Dense 2D matrix implementation designed for very fast access of entire rows.
class	SparseDoubleMatrix<R,C> A sparse matrix that knows about row and column names.
class	SparseRaggedDoubleMatrix<R,C> A sparse matrix class where the rows are ragged and compressed.

Methods in ubic.basecode.dataStructure.matrix that return DoubleMatrix

Modifier and Type	Method and Description
DoubleMatrix<R,C>	SparseRaggedDoubleMatrix.copy()
DoubleMatrix<R,C>	SparseDoubleMatrix.copy()
DoubleMatrix<R,C>	FastRowAccessDoubleMatrix.copy()
abstract DoubleMatrix<R,C>	DoubleMatrix.copy() Create a deep copy of this
DoubleMatrix<R,C>	DenseDoubleMatrix.copy()
DoubleMatrix<R,C>	CompressedSparseDoubleMatrix.copy()
DoubleMatrix<R,C>	SparseRaggedDoubleMatrix.getColRange(int startCol, int endCol)
DoubleMatrix<R,C>	SparseDoubleMatrix.getColRange(int startCol, int endCol)
DoubleMatrix<R,C>	FastRowAccessDoubleMatrix.getColRange(int startCol, int endCol)
abstract DoubleMatrix<R,C>	DoubleMatrix.getColRange(int startCol, int endCol)
DoubleMatrix<R,C>	DenseDoubleMatrix.getColRange(int startCol, int endCol)
DoubleMatrix<R,C>	CompressedSparseDoubleMatrix.getColRange(int startCol, int endCol)
DoubleMatrix<R,C>	SparseRaggedDoubleMatrix.getRowRange(int startRow, int endRow)
DoubleMatrix<R,C>	SparseDoubleMatrix.getRowRange(int startRow, int endRow)
DoubleMatrix<R,C>	FastRowAccessDoubleMatrix.getRowRange(int startRow, int endRow)
abstract DoubleMatrix<R,C>	DoubleMatrix.getRowRange(int startRow, int endRow)
DoubleMatrix<R,C>	DenseDoubleMatrix.getRowRange(int startRow, int endRow)
DoubleMatrix<R,C>	CompressedSparseDoubleMatrix.getRowRange(int startRow, int endRow)
DoubleMatrix<R,C>	SparseRaggedDoubleMatrix.subsetColumns(List<C> c)
DoubleMatrix<R,C>	SparseDoubleMatrix.subsetColumns(List<C> columns)
DoubleMatrix<R,C>	FastRowAccessDoubleMatrix.subsetColumns(List<C> columns)
abstract DoubleMatrix<R,C>	DoubleMatrix.subsetColumns(List<C> columns) Create a copy of this matrix with only the selected columns, in the selected order.
DoubleMatrix<R,C>	DenseDoubleMatrix.subsetColumns(List<C> columns)
DoubleMatrix<R,C>	CompressedSparseDoubleMatrix.subsetColumns(List<C> columns)
DoubleMatrix<R,C>	SparseRaggedDoubleMatrix.subsetRows(List<R> rowNames)
DoubleMatrix<R,C>	SparseDoubleMatrix.subsetRows(List<R> rowNames)
DoubleMatrix<R,C>	FastRowAccessDoubleMatrix.subsetRows(List<R> rowNames)
abstract DoubleMatrix<R,C>	DoubleMatrix.subsetRows(List<R> rowNames) Create a copy of this matrix with only the selected rows, in the selected order.
DoubleMatrix<R,C>	DenseDoubleMatrix.subsetRows(List<R> rowNames)
DoubleMatrix<R,C>	CompressedSparseDoubleMatrix.subsetRows(List<R> rowNames)
DoubleMatrix<C,R>	SparseRaggedDoubleMatrix.transpose()
DoubleMatrix<C,R>	SparseDoubleMatrix.transpose()
DoubleMatrix<C,R>	FastRowAccessDoubleMatrix.transpose()
abstract DoubleMatrix<C,R>	DoubleMatrix.transpose()
DoubleMatrix<C,R>	DenseDoubleMatrix.transpose()
DoubleMatrix<C,R>	CompressedSparseDoubleMatrix.transpose()

Methods in ubic.basecode.dataStructure.matrix with parameters of type DoubleMatrix

Modifier and Type	Method and Description
static DenseDoubleMatrix<String,String>	DoubleMatrixFactory.dense(DoubleMatrix<String,String> T) Creates a matrix in which the underlying data is a copy; the row and column labels are not copied.

Uses of DoubleMatrix in ubic.basecode.graphics

Fields in ubic.basecode.graphics declared as DoubleMatrix

Modifier and Type	Field and Description
protected DoubleMatrix<A,B>	ColorMatrix.maxtrix

Methods in ubic.basecode.graphics that return DoubleMatrix

Modifier and Type	Method and Description
DoubleMatrix<R,C>	MatrixDisplay.getMatrix()
DoubleMatrix<A,B>	ColorMatrix.getMatrix()
DoubleMatrix<A,B>	ColorMatrix.getMaxtrix()

Methods in ubic.basecode.graphics with parameters of type DoubleMatrix

Modifier and Type	Method and Description
static <R,C> ColorMatrix<R,C>	ColorMatrix.newInstance(DoubleMatrix<R,C> matrix)

Constructors in ubic.basecode.graphics with parameters of type DoubleMatrix

Constructor and Description
ColorMatrix(DoubleMatrix<A,B> matrix)
ColorMatrix(DoubleMatrix<A,B> matrix, Color[] colorMap, Color missingColor)
MatrixDisplay(DoubleMatrix<R,C> matrix)

Uses of DoubleMatrix in ubic.basecode.io.reader

Methods in ubic.basecode.io.reader that return DoubleMatrix

Modifier and Type	Method and Description
protected DoubleMatrix<String,String>	DoubleMatrixReader.createMatrix(List<cern.colt.list.DoubleArrayList> MTemp, List<String> rowNames, List<String> colNames1)
DoubleMatrix<String,String>	SparseDoubleMatrixReader.read(InputStream stream) Read a sparse matrix that is expressed as an adjacency list in a tab-delimited file: item1 item2 weight item1 item5 weight By definition the resulting matrix is square and symmetric.
DoubleMatrix<String,String>	DoubleMatrixReader.read(InputStream stream)
DoubleMatrix<String,String>	SparseDoubleMatrixReader.read(InputStream stream, Collection<String> wantedRowNames)
DoubleMatrix<String,String>	DoubleMatrixReader.read(InputStream stream, Collection<String> wantedRowNames)
DoubleMatrix<String,String>	SparseDoubleMatrixReader.read(InputStream stream, Collection<String> wantedRowNames, boolean createEmptyRows, int skipColumns, int maxRows)
DoubleMatrix<String,String>	DoubleMatrixReader.read(InputStream stream, Collection<String> wantedRowNames, boolean createEmptyRows, int skipColumns, int maxRows)
DoubleMatrix<String,String>	DoubleMatrixReader.read(InputStream stream, Collection<String> wantedRowNames, int numberOfColumnsToSkip)
DoubleMatrix<String,String>	SparseRaggedMatrixReader.read(InputStream stream, int offset) Read an entire sparse matrix from a stream (JW format).
DoubleMatrix<String,String>	DoubleMatrixReader.read(String filename)
DoubleMatrix<String,String>	DoubleMatrixReader.read(String filename, Collection<String> wantedRowNames) Read a matrix from a file, subject to filtering criteria.
DoubleMatrix<String,String>	DoubleMatrixReader.read(String fileName, Collection<String> wantedRowNames, int numberOfColumnsToSkip)
DoubleMatrix<String,String>	DoubleMatrixReader.read(String filename, int maxRows)
DoubleMatrix<String,String>	SparseRaggedMatrixReader.readFromAdjList(InputStream stream)
DoubleMatrix<String,String>	SparseRaggedMatrixReader.readFromAdjList(String fileName) Read a sparse symmetric square matrix that is expressed as an adjacency list in a tab-delimited file: item1 item2 weight item1 item5 weight IMPORTANT: By definition the resulting matrix is square and symmetric, even if the symmetric edges are not explicitly listed.
DoubleMatrix<String,String>	SparseDoubleMatrixReader.readJW(InputStream stream) Read a sparse matrix in "JW" (Jason Weston) format.
DoubleMatrix<String,String>	SparseRaggedMatrixReader.readOneRow(BufferedReader dis, int offset) Use this to read one row from a matrix (JW format).

Uses of DoubleMatrix in ubic.basecode.math

Methods in ubic.basecode.math that return DoubleMatrix

Modifier and Type	Method and Description
static <R,C> DoubleMatrix<R,C>	MatrixStats.convertToLog2Cpm(DoubleMatrix<R,C> matrix, cern.colt.matrix.DoubleMatrix1D librarySize) Convert a count matrix to log2 counts per million.
static <R,C> DoubleMatrix<R,R>	MatrixStats.correlationMatrix(DoubleMatrix<R,C> data) Compute the correlation matrix of the rows of a matrix.
static <R,C> DoubleMatrix<R,C>	MatrixStats.doubleStandardize(DoubleMatrix<R,C> matrix) Iteratively standardize the columns and rows of the matrix.
DoubleMatrix<R,C>	MatrixNormalizer.quantileNormalize(DoubleMatrix<R,C> matrix) Rows with all missing will not be returned.
static <R,C> DoubleMatrix<R,C>	MatrixStats.standardize(DoubleMatrix<R,C> matrix) Scale the rows of the matrix; returns a new matrix.

Methods in ubic.basecode.math with parameters of type DoubleMatrix

Modifier and Type	Method and Description
static <R,C> cern.colt.matrix.DoubleMatrix1D	MatrixStats.colSums(DoubleMatrix<R,C> data) NaN values are omitted from calculations.
static <R,C> void	MatrixStats.convertToLog2(DoubleMatrix<R,C> matrix, double base) Convert a log_b-transformed data set to log 2.
static <R,C> DoubleMatrix<R,C>	MatrixStats.convertToLog2Cpm(DoubleMatrix<R,C> matrix, cern.colt.matrix.DoubleMatrix1D librarySize) Convert a count matrix to log2 counts per million.
static <R,C> DoubleMatrix<R,R>	MatrixStats.correlationMatrix(DoubleMatrix<R,C> data) Compute the correlation matrix of the rows of a matrix.
static <R,C> SparseDoubleMatrix<R,R>	MatrixStats.correlationMatrix(DoubleMatrix<R,C> data, double threshold)
static <R,C> DoubleMatrix<R,C>	MatrixStats.doubleStandardize(DoubleMatrix<R,C> matrix) Iteratively standardize the columns and rows of the matrix.
static <R,C> void	MatrixStats.logTransform(DoubleMatrix<R,C> matrix) Log-transform the values in a matrix (log base 2).
static <R,C> double	MatrixStats.max(DoubleMatrix<R,C> matrix) Compute the maximum value in the matrix.
static <R,C> cern.colt.list.DoubleArrayList	MatrixRowStats.means(DoubleMatrix<R,C> M) Calculates the means of a matrix's rows.
static <R,C> double	MatrixStats.min(DoubleMatrix<R,C> matrix) Find the minimum of the entire matrix.
DoubleMatrix<R,C>	MatrixNormalizer.quantileNormalize(DoubleMatrix<R,C> matrix) Rows with all missing will not be returned.
static <R,C> void	MatrixStats.rbfNormalize(DoubleMatrix<R,C> matrixToNormalize, double sigma) Normalize a matrix in place to be a transition matrix.
static <R,C> cern.colt.list.DoubleArrayList	MatrixRowStats.sampleStandardDeviations(DoubleMatrix<R,C> M) Calculates the sample standard deviation of each row of a matrix
static <R,C> DoubleMatrix<R,C>	MatrixStats.standardize(DoubleMatrix<R,C> matrix) Scale the rows of the matrix; returns a new matrix.
static <R,C> cern.colt.list.DoubleArrayList	MatrixRowStats.sumOfSquares(DoubleMatrix<R,C> M) Calculates the sum of squares for each row of a matrix
static <R,C> cern.colt.list.DoubleArrayList	MatrixRowStats.sums(DoubleMatrix<R,C> M) Calculate the sums of a matrix's rows.
static <R,C> void	MatrixStats.unLogTransform(DoubleMatrix<R,C> matrix) Undo log2 transform.

Uses of DoubleMatrix in ubic.basecode.math.linalg

Methods in ubic.basecode.math.linalg that return DoubleMatrix

Modifier and Type	Method and Description
DoubleMatrix<Integer,Integer>	SingularValueDecomposition.getS()
DoubleMatrix<R,Integer>	SingularValueDecomposition.getU()
DoubleMatrix<Integer,C>	SingularValueDecomposition.getV()

Constructors in ubic.basecode.math.linalg with parameters of type DoubleMatrix

Constructor and Description
SingularValueDecomposition(DoubleMatrix<R,C> matrix)

Uses of DoubleMatrix in ubic.basecode.math.linearmodels

Methods in ubic.basecode.math.linearmodels that return DoubleMatrix

Modifier and Type	Method and Description
DoubleMatrix<String,String>	LinearModelSummary.getContrastCoefficients()
DoubleMatrix<String,String>	DesignMatrix.getMatrix()

Constructors in ubic.basecode.math.linearmodels with parameters of type DoubleMatrix

Constructor and Description
LeastSquaresFit(DesignMatrix designMatrix, DoubleMatrix<String,String> data) Preferred interface if you want control over how the design is set up.
LeastSquaresFit(DesignMatrix designMatrix, DoubleMatrix<String,String> data, cern.colt.matrix.DoubleMatrix2D weights) Weighted least squares fit between two matrices
LeastSquaresFit(ObjectMatrix<String,String,Object> design, DoubleMatrix<String,String> b) NamedMatrix allows easier handling of the results.
LeastSquaresFit(ObjectMatrix<String,String,Object> design, DoubleMatrix<String,String> data, boolean interactions) NamedMatrix allows easier handling of the results.
LinearModelSummary(String k, Double[] coefficients, Double[] residuals, List<String> terms, DoubleMatrix<String,String> contrastCoefficients, Double[] effects, Double[] stdevUnscaled, double rsquared, double adjRsquared, double fstat, Integer ndof, Integer ddof, GenericAnovaResult anovaResult, double sigma, boolean isShrunken)
MeanVarianceEstimator(DesignMatrix designMatrix, DoubleMatrix<String,String> data, cern.colt.matrix.DoubleMatrix1D librarySize) Preferred interface if you want control over how the design is set up.

Uses of DoubleMatrix in ubic.basecode.util

Methods in ubic.basecode.util with parameters of type DoubleMatrix

Modifier and Type	Method and Description
static boolean	RegressionTesting.closeEnough(DoubleMatrix<?,?> expected, DoubleMatrix<?,?> actual, double tolerance) Test whether two AbstractNamedDoubleMatrix are 'close enough' to call equal.
static boolean	RegressionTesting.closeEnough(DoubleMatrix<?,?> expected, DoubleMatrix<?,?> actual, double tolerance) Test whether two AbstractNamedDoubleMatrix are 'close enough' to call equal.

Uses of DoubleMatrix in ubic.basecode.util.r

Methods in ubic.basecode.util.r that return DoubleMatrix

Modifier and Type	Method and Description
DoubleMatrix<String,String>	RClient.retrieveMatrix(String variableName) Get a matrix back out of the R context.
DoubleMatrix<String,String>	JRIClient.retrieveMatrix(String variableName)
DoubleMatrix<String,String>	RServeClient.retrieveMatrix(String variableName)

Methods in ubic.basecode.util.r with parameters of type DoubleMatrix

Modifier and Type	Method and Description
String	RClient.assignMatrix(DoubleMatrix<?,?> matrix) Assign a 2-d matrix.
String	AbstractRClient.assignMatrix(DoubleMatrix<?,?> matrix)
String	RClient.assignMatrix(DoubleMatrix<?,?> matrix, org.apache.commons.collections4.Transformer rowNameExtractor) Assign a 2-d matrix.
String	AbstractRClient.assignMatrix(DoubleMatrix<?,?> matrix, org.apache.commons.collections4.Transformer rowNameExtractor)