Inheritance diagram for broad.core.datastructures.MatrixWithHeaders:

Public Member Functions
	MatrixWithHeaders (String inputFile) throws IOException, ParseException

	MatrixWithHeaders (BufferedReader br) throws IOException, ParseException

	MatrixWithHeaders (Matrix data, List< String > rowNames, List< String > colNames)

	MatrixWithHeaders (Matrix data, List< String > rowNames, List< String > colNames, List< String > rowDescriptions)

	MatrixWithHeaders (List< String > rows, List< String > columns, Map< String, String > pidToName)

	MatrixWithHeaders (MatrixWithHeaders matrix, List< String > rows, List< String > columns)

	MatrixWithHeaders (List< String > rows, List< String > columns)

	MatrixWithHeaders (List< String > rows, List< String > columns, List< String > rowDescriptions)

	MatrixWithHeaders (String gctFile, String chipFile) throws IOException, ParseException

	MatrixWithHeaders (List< List< Double >> rawData, ArrayList< String > rowNameList, List< String > columnNameList)

	MatrixWithHeaders (ArrayList< String > rows, ArrayList< String > columns, int DefMatVal)

Map< String, String >	getPIDToName ()

void	write (BufferedWriter bw) throws IOException

void	write (String fileName) throws IOException

void	writeGCT (BufferedWriter bw) throws IOException

void	writeGCT (String save) throws IOException

void	writeGCT (String save, Collection< String > columns) throws IOException

void	writeGCT (String save, Map< String, Collection< String >> experimentInfo, boolean ordered) throws IOException

void	writeGCT (String save, Map< String, Collection< String >> experimentInfo, Map< String, ExpressionExperimentInfo > fullInfo, boolean info) throws IOException

void	writeGCT (String save, Collection< String > columns, Collection< String > rows) throws IOException

void	writeGCTWithHeaders (String save, Map< String, String > columnMapping) throws IOException

void	writeGCT (String save, Collection< String > columns, Collection< String > rows, int precision) throws IOException

void	writeGCT (String save, Map< String, String > columns, Map< String, String > rows) throws IOException

void	writeGCT (String save, Map< String, String > columns, Collection< String > rows) throws IOException

void	writeGCT (String save, Map< String, String > columns) throws IOException

void	writeGCT (String save, File chipFile) throws IOException

Matrix	dataInverse ()

int	columnDimension ()

int	rowDimension ()

double	get (int i, int j)

double[]	getColumn (int j)

double[]	getColumn (String columnName)

double[]	getRow (String rowName)

void	set (int i, int j, double val)

void	set (String row, String column, double value)

void	setRow (String row, double[] vals)

void	setColumn (double[] vals, String column)

void	setColumn (double[] vals, int column)

void	set (String row, int colIdx, double value)

void	set (int rowIdx, String column, double value)

double	get (String row, String column)

boolean	containsColumn (String colName)

boolean	containsRow (String rowName)

double	get (String rowName, int colIdx)

double	get (int rowIdx, String colName)

List< String >	getColumnNames ()

List< String >	getRowNames ()

String	getRowName (int i)

String	getColoumnName (int i)

List< String >	getRowDescriptions ()

boolean	hasColumn (String column)

boolean	hasRow (String row)

List< Integer >	getIndecesForRowDescription (String rowDescription)

void	setRowDescription (int rowIdx, String rowDescription)

void	setRowDescription (String row, String rowDescription)

MatrixWithHeaders	filterValuesLargerThanUsingColumn (int colIdx, double maxValue)

MatrixWithHeaders	filterValuesSmallerThanUsingColumn (int colIdx, double minValue)

MatrixWithHeaders	filterValuesRangeUsingColumn (int colIdx, double minVal, double maxVal)

boolean	isColumnNonTrivial (String colName)

void	compressMatrixByRowDescriptions ()

void	normalizeByMean ()

void	zColumnNormalize ()

void	zRowNormalize ()

void	normalizeBy (double constant)

void	normalizeColumnsByMean ()

void	normalizeColumnsByMedian ()

MatrixWithHeaders	submatrixByRowDescriptions (Collection< String > rowDescriptions, List< String > newRowNames)

MatrixWithHeaders	submatrixByRowNames (Collection< String > rowNames)

MatrixWithHeaders	submatrixByRowNames (String rowName)

MatrixWithHeaders	submatrixByRowNames (String[] rowNames)

MatrixWithHeaders	submatrixByColumnNames (Collection< String > columnNames)

MatrixWithHeaders	submatrixByColumnIndex (Collection< Integer > columnIndex)

MatrixWithHeaders	submatrixByColumnNames (String[] columnNames)

MatrixWithHeaders	zScoresByColumn (List< String > controlRows)

MatrixWithHeaders	tScoresByRow (List< Integer > controlRows, List< Integer > sampleRows, String comparisonName, double fudgeFactor)

MatrixWithHeaders	rank ()

void	quantileNormalizeColumns ()

MatrixWithHeaders	confidenceByColumn (List< String > controlRows)

MatrixWithHeaders	sortList (int columnIndex)

void	append (MatrixWithHeaders other)

void	appendColumns (MatrixWithHeaders other)

void	appendRows (MatrixWithHeaders other)

void	add (MatrixWithHeaders m2)

void	log2 ()

void	log2 (double fudge)

void	log10 ()

void	log10 (double fudge)

void	pow ()

void	round ()

MatrixWithHeaders	times (MatrixWithHeaders other)

void	minus (MatrixWithHeaders other)

Matrix	getData ()

Map< String, Collection < Integer > >	getNanostringReplicateMap ()

Map< String, String >	getNanostringProbeClasses ()

int	getNumberColumns ()

int	getNumberRows ()

Map< String, double[]>	toMap ()

void	writeGMT (String save, double fold) throws IOException

MatrixWithHeaders	quantileNormalize ()

MatrixWithHeaders	copy ()

MatrixWithHeaders	medianCenterColumns ()

MatrixWithHeaders	medianCenterRows ()

void	medianCenterColumnsThis ()

void	medianCenterRowsThis ()

void	meanNormalizeColumns () throws IllegalStateException

void	medianNormalizeColumns () throws IllegalStateException

void	meanNormalizeRows () throws IllegalStateException

void	medianNormalizeRows () throws IllegalStateException

MatrixWithHeaders	scaleNorm ()

void	columnDensityNormalization () throws IllegalStateException

void	rowDensityNormalization () throws IllegalStateException

void	setPIDToName (Map< String, String > rowDescriptions)

void	writeCLS (String string, Collection< String > subset, Collection< String > negatives) throws IOException

void	writeGCTAndCLS (String save, Map< String, ExpressionExperimentInfo > experimentInfo) throws IOException

void	randomPermuteColumns ()

void	addRow (String row, String description, double[] vals)

void	addColumn (String column)

MatrixWithHeaders	filterInvariantGenes (MatrixWithHeaders data, double fold)

void	writeBox (String save) throws IOException

MatrixWithHeaders	excludeByRowNames (Collection< String > flaggedGenes)

double[]	getRow (int i)

void	floor (double floor)

void	writeRowNamesToFile (String outFile) throws IOException

void	writeColoumnNamesToFile (String outFile) throws IOException

double[]	getMedianOverAllRows ()

double[]	getMeanOverAllRows ()

double[]	getRow (String gene, Collection< String > group1)

double[]	getValues (String gene, Collection< String > controls)

boolean	hasNanostringProbeClasses ()

MatrixWithHeaders	multiplyColumnsWithConstants (double[] constants)

MatrixWithHeaders	multiplyColumnsWithConstants (Map< String, Double > constants)

Protected Member Functions
	MatrixWithHeaders ()

void	initFromReader (BufferedReader br) throws IOException, ParseException

void	initFromRegularMatrix (BufferedReader br, String header) throws IOException, ParseException

void	initGCTFromReader (BufferedReader br) throws IOException, ParseException

void	initFromNanostring (BufferedReader br, String header) throws IOException, ParseException

void	initNameIndexMaps (List< String > rowNameList, List< String > columnNameList)

void	setData (Matrix data)

void	initRowIndexMaps (List< String > rowNameList)

void	initColIndexMaps (List< String > columnNameList)

void	initRowDescrIndexMaps (List< String > rowDescriptionList)

Constructor & Destructor Documentation

broad.core.datastructures.MatrixWithHeaders.MatrixWithHeaders ( )

protected

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broad.core.datastructures.MatrixWithHeaders.MatrixWithHeaders ( String inputFile ) throws IOException, ParseException

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broad.core.datastructures.MatrixWithHeaders.MatrixWithHeaders ( BufferedReader br ) throws IOException, ParseException

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broad.core.datastructures.MatrixWithHeaders.MatrixWithHeaders	(	Matrix	data,
		List< String >	rowNames,
		List< String >	colNames
	)

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broad.core.datastructures.MatrixWithHeaders.MatrixWithHeaders	(	Matrix	data,
		List< String >	rowNames,
		List< String >	colNames,
		List< String >	rowDescriptions
	)

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broad.core.datastructures.MatrixWithHeaders.MatrixWithHeaders	(	List< String >	rows,
		List< String >	columns,
		Map< String, String >	pidToName
	)

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broad.core.datastructures.MatrixWithHeaders.MatrixWithHeaders	(	MatrixWithHeaders	matrix,
		List< String >	rows,
		List< String >	columns
	)

Create a new matrix that has a subset of columns and rows of the original matrix

Parameters

matrix
colsInRows
colsInRows2

broad.core.datastructures.MatrixWithHeaders.MatrixWithHeaders	(	List< String >	rows,
		List< String >	columns
	)

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broad.core.datastructures.MatrixWithHeaders.MatrixWithHeaders	(	List< String >	rows,
		List< String >	columns,
		List< String >	rowDescriptions
	)

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broad.core.datastructures.MatrixWithHeaders.MatrixWithHeaders	(	String	gctFile,
		String	chipFile
	)		throws IOException, ParseException

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broad.core.datastructures.MatrixWithHeaders.MatrixWithHeaders	(	List< List< Double >>	rawData,
		ArrayList< String >	rowNameList,
		List< String >	columnNameList
	)

broad.core.datastructures.MatrixWithHeaders.MatrixWithHeaders	(	ArrayList< String >	rows,
		ArrayList< String >	columns,
		int	DefMatVal
	)

Member Function Documentation

void broad.core.datastructures.MatrixWithHeaders.add ( MatrixWithHeaders m2 )

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void broad.core.datastructures.MatrixWithHeaders.addColumn ( String column )

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void broad.core.datastructures.MatrixWithHeaders.addRow	(	String	row,
		String	description,
		double[]	vals
	)

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void broad.core.datastructures.MatrixWithHeaders.append ( MatrixWithHeaders other )

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void broad.core.datastructures.MatrixWithHeaders.appendColumns ( MatrixWithHeaders other )

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void broad.core.datastructures.MatrixWithHeaders.appendRows ( MatrixWithHeaders other )

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void broad.core.datastructures.MatrixWithHeaders.columnDensityNormalization ( ) throws IllegalStateException

Normalizes each column so it adds up to 1

Exceptions

IllegalStateException if a column contains negative numbers

int broad.core.datastructures.MatrixWithHeaders.columnDimension ( )

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void broad.core.datastructures.MatrixWithHeaders.compressMatrixByRowDescriptions ( )

Replaces each set of rows with same description with a row with column values the mean of the original row column values

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MatrixWithHeaders broad.core.datastructures.MatrixWithHeaders.confidenceByColumn ( List< String > controlRows )

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boolean broad.core.datastructures.MatrixWithHeaders.containsColumn ( String colName )

boolean broad.core.datastructures.MatrixWithHeaders.containsRow ( String rowName )

MatrixWithHeaders broad.core.datastructures.MatrixWithHeaders.copy ( )

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Matrix broad.core.datastructures.MatrixWithHeaders.dataInverse ( )

Takes the inverse (or pseudo inverse if the underlying data is not a squared matrix)

Returns

MatrixWithHeaders broad.core.datastructures.MatrixWithHeaders.excludeByRowNames ( Collection< String > flaggedGenes )

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MatrixWithHeaders broad.core.datastructures.MatrixWithHeaders.filterInvariantGenes	(	MatrixWithHeaders	data,
		double	fold
	)

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MatrixWithHeaders broad.core.datastructures.MatrixWithHeaders.filterValuesLargerThanUsingColumn	(	int	colIdx,
		double	maxValue
	)

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MatrixWithHeaders broad.core.datastructures.MatrixWithHeaders.filterValuesRangeUsingColumn	(	int	colIdx,
		double	minVal,
		double	maxVal
	)

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MatrixWithHeaders broad.core.datastructures.MatrixWithHeaders.filterValuesSmallerThanUsingColumn	(	int	colIdx,
		double	minValue
	)

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void broad.core.datastructures.MatrixWithHeaders.floor ( double floor )

Resets all values below floor to floor.

Parameters

floor

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double broad.core.datastructures.MatrixWithHeaders.get	(	int	i,
		int	j
	)

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double broad.core.datastructures.MatrixWithHeaders.get	(	String	row,
		String	column
	)

double broad.core.datastructures.MatrixWithHeaders.get	(	String	rowName,
		int	colIdx
	)

double broad.core.datastructures.MatrixWithHeaders.get	(	int	rowIdx,
		String	colName
	)

String broad.core.datastructures.MatrixWithHeaders.getColoumnName ( int i )

double [] broad.core.datastructures.MatrixWithHeaders.getColumn ( int j )

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double [] broad.core.datastructures.MatrixWithHeaders.getColumn ( String columnName )

List<String> broad.core.datastructures.MatrixWithHeaders.getColumnNames ( )

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Matrix broad.core.datastructures.MatrixWithHeaders.getData ( )

List<Integer> broad.core.datastructures.MatrixWithHeaders.getIndecesForRowDescription ( String rowDescription )

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double [] broad.core.datastructures.MatrixWithHeaders.getMeanOverAllRows ( )

double [] broad.core.datastructures.MatrixWithHeaders.getMedianOverAllRows ( )

Map<String, String> broad.core.datastructures.MatrixWithHeaders.getNanostringProbeClasses ( )

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Map<String, Collection<Integer> > broad.core.datastructures.MatrixWithHeaders.getNanostringReplicateMap ( )

int broad.core.datastructures.MatrixWithHeaders.getNumberColumns ( )

int broad.core.datastructures.MatrixWithHeaders.getNumberRows ( )

Map<String, String> broad.core.datastructures.MatrixWithHeaders.getPIDToName ( )

double [] broad.core.datastructures.MatrixWithHeaders.getRow ( String rowName )

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double [] broad.core.datastructures.MatrixWithHeaders.getRow ( int i )

double [] broad.core.datastructures.MatrixWithHeaders.getRow	(	String	gene,
		Collection< String >	group1
	)

List<String> broad.core.datastructures.MatrixWithHeaders.getRowDescriptions ( )

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String broad.core.datastructures.MatrixWithHeaders.getRowName ( int i )

List<String> broad.core.datastructures.MatrixWithHeaders.getRowNames ( )

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double [] broad.core.datastructures.MatrixWithHeaders.getValues	(	String	gene,
		Collection< String >	controls
	)

boolean broad.core.datastructures.MatrixWithHeaders.hasColumn ( String column )

boolean broad.core.datastructures.MatrixWithHeaders.hasNanostringProbeClasses ( )

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boolean broad.core.datastructures.MatrixWithHeaders.hasRow ( String row )

void broad.core.datastructures.MatrixWithHeaders.initColIndexMaps ( List< String > columnNameList )

protected

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void broad.core.datastructures.MatrixWithHeaders.initFromNanostring	(	BufferedReader	br,
		String	header
	)		throws IOException, ParseException

protected

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void broad.core.datastructures.MatrixWithHeaders.initFromReader ( BufferedReader br ) throws IOException, ParseException

protected

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void broad.core.datastructures.MatrixWithHeaders.initFromRegularMatrix	(	BufferedReader	br,
		String	header
	)		throws IOException, ParseException

protected

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void broad.core.datastructures.MatrixWithHeaders.initGCTFromReader ( BufferedReader br ) throws IOException, ParseException

protected

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void broad.core.datastructures.MatrixWithHeaders.initNameIndexMaps	(	List< String >	rowNameList,
		List< String >	columnNameList
	)

protected

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void broad.core.datastructures.MatrixWithHeaders.initRowDescrIndexMaps ( List< String > rowDescriptionList )

protected

void broad.core.datastructures.MatrixWithHeaders.initRowIndexMaps ( List< String > rowNameList )

protected

boolean broad.core.datastructures.MatrixWithHeaders.isColumnNonTrivial ( String colName )

returns true if the column has a nonzero value

void broad.core.datastructures.MatrixWithHeaders.log10 ( )

void broad.core.datastructures.MatrixWithHeaders.log10 ( double fudge )

void broad.core.datastructures.MatrixWithHeaders.log2 ( )

void broad.core.datastructures.MatrixWithHeaders.log2 ( double fudge )

void broad.core.datastructures.MatrixWithHeaders.meanNormalizeColumns ( ) throws IllegalStateException

Substitutes each value in a column with the ratio of the value and the mean of column value Only applicable to positive value matrices.

void broad.core.datastructures.MatrixWithHeaders.meanNormalizeRows ( ) throws IllegalStateException

Substitutes each value in a row with the ratio of the value and the mean of row value Only applicable to positive value matrices.

MatrixWithHeaders broad.core.datastructures.MatrixWithHeaders.medianCenterColumns ( )

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void broad.core.datastructures.MatrixWithHeaders.medianCenterColumnsThis ( )

Mean centers the columns of the current matrix rather than creating a new one.

MatrixWithHeaders broad.core.datastructures.MatrixWithHeaders.medianCenterRows ( )

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void broad.core.datastructures.MatrixWithHeaders.medianCenterRowsThis ( )

Mean centers the rows of the current matrix rather than creating a new one.

void broad.core.datastructures.MatrixWithHeaders.medianNormalizeColumns ( ) throws IllegalStateException

Substitutes each value in a column with the ratio of the value and the mean of column value Only applicable to positive value matrices.

void broad.core.datastructures.MatrixWithHeaders.medianNormalizeRows ( ) throws IllegalStateException

Substitutes each value in a row with the ratio of the value and the mean of row value Only applicable to positive value matrices.

void broad.core.datastructures.MatrixWithHeaders.minus ( MatrixWithHeaders other )

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MatrixWithHeaders broad.core.datastructures.MatrixWithHeaders.multiplyColumnsWithConstants ( double[] constants )

Author: skadri Multiplies each column with a separate constant. That is, given a vector (dimension same as number of columns) multiplies all rows of column with same constant

Returns

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MatrixWithHeaders broad.core.datastructures.MatrixWithHeaders.multiplyColumnsWithConstants ( Map< String, Double > constants )

Author: skadri Multiplies each column with a separate constant. That is, given a vector (dimension same as number of columns) multiplies all rows of column with same constant

Returns

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void broad.core.datastructures.MatrixWithHeaders.normalizeBy ( double constant )

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void broad.core.datastructures.MatrixWithHeaders.normalizeByMean ( )

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void broad.core.datastructures.MatrixWithHeaders.normalizeColumnsByMean ( )

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void broad.core.datastructures.MatrixWithHeaders.normalizeColumnsByMedian ( )

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void broad.core.datastructures.MatrixWithHeaders.pow ( )

MatrixWithHeaders broad.core.datastructures.MatrixWithHeaders.quantileNormalize ( )

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void broad.core.datastructures.MatrixWithHeaders.quantileNormalizeColumns ( )

void broad.core.datastructures.MatrixWithHeaders.randomPermuteColumns ( )

MatrixWithHeaders broad.core.datastructures.MatrixWithHeaders.rank ( )

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void broad.core.datastructures.MatrixWithHeaders.round ( )

void broad.core.datastructures.MatrixWithHeaders.rowDensityNormalization ( ) throws IllegalStateException

Normalizes each row so it adds up to 1

Exceptions

IllegalStateException if a column contains negative numbers

int broad.core.datastructures.MatrixWithHeaders.rowDimension ( )

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MatrixWithHeaders broad.core.datastructures.MatrixWithHeaders.scaleNorm ( )

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void broad.core.datastructures.MatrixWithHeaders.set	(	int	i,
		int	j,
		double	val
	)

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void broad.core.datastructures.MatrixWithHeaders.set	(	String	row,
		String	column,
		double	value
	)

void broad.core.datastructures.MatrixWithHeaders.set	(	String	row,
		int	colIdx,
		double	value
	)

void broad.core.datastructures.MatrixWithHeaders.set	(	int	rowIdx,
		String	column,
		double	value
	)

void broad.core.datastructures.MatrixWithHeaders.setColumn	(	double[]	vals,
		String	column
	)

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void broad.core.datastructures.MatrixWithHeaders.setColumn	(	double[]	vals,
		int	column
	)

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void broad.core.datastructures.MatrixWithHeaders.setData ( Matrix data )

protected

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void broad.core.datastructures.MatrixWithHeaders.setPIDToName ( Map< String, String > rowDescriptions )

void broad.core.datastructures.MatrixWithHeaders.setRow	(	String	row,
		double[]	vals
	)

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void broad.core.datastructures.MatrixWithHeaders.setRowDescription	(	int	rowIdx,
		String	rowDescription
	)

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void broad.core.datastructures.MatrixWithHeaders.setRowDescription	(	String	row,
		String	rowDescription
	)

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MatrixWithHeaders broad.core.datastructures.MatrixWithHeaders.sortList ( int columnIndex )

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MatrixWithHeaders broad.core.datastructures.MatrixWithHeaders.submatrixByColumnIndex ( Collection< Integer > columnIndex )

MatrixWithHeaders broad.core.datastructures.MatrixWithHeaders.submatrixByColumnNames ( Collection< String > columnNames )

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MatrixWithHeaders broad.core.datastructures.MatrixWithHeaders.submatrixByColumnNames ( String[] columnNames )

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MatrixWithHeaders broad.core.datastructures.MatrixWithHeaders.submatrixByRowDescriptions	(	Collection< String >	rowDescriptions,
		List< String >	newRowNames
	)

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MatrixWithHeaders broad.core.datastructures.MatrixWithHeaders.submatrixByRowNames ( Collection< String > rowNames )

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MatrixWithHeaders broad.core.datastructures.MatrixWithHeaders.submatrixByRowNames ( String rowName )

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MatrixWithHeaders broad.core.datastructures.MatrixWithHeaders.submatrixByRowNames ( String[] rowNames )

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MatrixWithHeaders broad.core.datastructures.MatrixWithHeaders.times ( MatrixWithHeaders other )

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Map<String, double[]> broad.core.datastructures.MatrixWithHeaders.toMap ( )

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MatrixWithHeaders broad.core.datastructures.MatrixWithHeaders.tScoresByRow	(	List< Integer >	controlRows,
		List< Integer >	sampleRows,
		String	comparisonName,
		double	fudgeFactor
	)

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void broad.core.datastructures.MatrixWithHeaders.write ( BufferedWriter bw ) throws IOException

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void broad.core.datastructures.MatrixWithHeaders.write ( String fileName ) throws IOException

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void broad.core.datastructures.MatrixWithHeaders.writeBox ( String save ) throws IOException

void broad.core.datastructures.MatrixWithHeaders.writeCLS	(	String	string,
		Collection< String >	subset,
		Collection< String >	negatives
	)		throws IOException

void broad.core.datastructures.MatrixWithHeaders.writeColoumnNamesToFile ( String outFile ) throws IOException

void broad.core.datastructures.MatrixWithHeaders.writeGCT ( BufferedWriter bw ) throws IOException

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void broad.core.datastructures.MatrixWithHeaders.writeGCT ( String save ) throws IOException

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void broad.core.datastructures.MatrixWithHeaders.writeGCT	(	String	save,
		Collection< String >	columns
	)		throws IOException

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void broad.core.datastructures.MatrixWithHeaders.writeGCT	(	String	save,
		Map< String, Collection< String >>	experimentInfo,
		boolean	ordered
	)		throws IOException

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void broad.core.datastructures.MatrixWithHeaders.writeGCT	(	String	save,
		Map< String, Collection< String >>	experimentInfo,
		Map< String, ExpressionExperimentInfo >	fullInfo,
		boolean	info
	)		throws IOException

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void broad.core.datastructures.MatrixWithHeaders.writeGCT	(	String	save,
		Collection< String >	columns,
		Collection< String >	rows
	)		throws IOException

void broad.core.datastructures.MatrixWithHeaders.writeGCT	(	String	save,
		Collection< String >	columns,
		Collection< String >	rows,
		int	precision
	)		throws IOException

void broad.core.datastructures.MatrixWithHeaders.writeGCT	(	String	save,
		Map< String, String >	columns,
		Map< String, String >	rows
	)		throws IOException

void broad.core.datastructures.MatrixWithHeaders.writeGCT	(	String	save,
		Map< String, String >	columns,
		Collection< String >	rows
	)		throws IOException

void broad.core.datastructures.MatrixWithHeaders.writeGCT	(	String	save,
		Map< String, String >	columns
	)		throws IOException

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void broad.core.datastructures.MatrixWithHeaders.writeGCT	(	String	save,
		File	chipFile
	)		throws IOException

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void broad.core.datastructures.MatrixWithHeaders.writeGCTAndCLS	(	String	save,
		Map< String, ExpressionExperimentInfo >	experimentInfo
	)		throws IOException

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void broad.core.datastructures.MatrixWithHeaders.writeGCTWithHeaders	(	String	save,
		Map< String, String >	columnMapping
	)		throws IOException

void broad.core.datastructures.MatrixWithHeaders.writeGMT	(	String	save,
		double	fold
	)		throws IOException

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void broad.core.datastructures.MatrixWithHeaders.writeRowNamesToFile ( String outFile ) throws IOException

void broad.core.datastructures.MatrixWithHeaders.zColumnNormalize ( )

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void broad.core.datastructures.MatrixWithHeaders.zRowNormalize ( )

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MatrixWithHeaders broad.core.datastructures.MatrixWithHeaders.zScoresByColumn ( List< String > controlRows )

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The documentation for this class was generated from the following file:

java/broad/core/datastructures/MatrixWithHeaders.java

Public Member Functions

Protected Member Functions

Constructor & Destructor Documentation

Member Function Documentation