Inheritance diagram for broad.pda.datastructures.LocationAwareMatrix:

Collaboration diagram for broad.pda.datastructures.LocationAwareMatrix:

Public Member Functions
	LocationAwareMatrix ()

	LocationAwareMatrix (List< String > rows, List< String > columns, Map< String, LightweightGenomicAnnotation > rowLocations)

	LocationAwareMatrix (BufferedReader br, String chr) throws IOException, ParseException

	LocationAwareMatrix (List<?extends LightweightGenomicAnnotation > probeData, List< String > samples)

	LocationAwareMatrix (MatrixWithHeaders mwh)

Set< String >	getChromosomes ()

LightweightGenomicAnnotation	getRowPosition (String row)

void	setColumns (List< String > columns)

void	setDataDimensions (int rowDim, int columnDim)

Collection < LightweightGenomicAnnotation >	getRowAnnotations ()

void	write (BufferedWriter bw) throws IOException

void	annotation (GenomicAnnotation annotation)

void	eof ()

void	begin ()

IntervalTree< String >	getRowTree (String chromosome)

LocationAwareMatrix	submatrixByColumns (Collection< String > columnNames)

LocationAwareMatrix	submatrixByColumns (String[] columnNames)

List < LightweightGenomicAnnotation >	getOverlappers (LightweightGenomicAnnotation annotation)

void	browserLine (String line)

void	track (String line)

LocationAwareMatrix	removeOverlappingRows (LocationAwareMatrix other)

void	appendRows (LocationAwareMatrix other)

Map< String, LightweightGenomicAnnotation >	getRowLocationMap ()

LightweightGenomicAnnotation	getClosest (LightweightGenomicAnnotation annotation)

LightweightGenomicAnnotation	getPriorClosest (LightweightGenomicAnnotation annotation)

LightweightGenomicAnnotation	getNextClosest (LightweightGenomicAnnotation annotation)

Public Member Functions inherited from broad.core.datastructures.MatrixWithHeaders
	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
void	initFromIGVMatrix (BufferedReader br, String header, String chromosomeToLoad) throws IOException, ParseException

Protected Member Functions inherited from broad.core.datastructures.MatrixWithHeaders
	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.pda.datastructures.LocationAwareMatrix.LocationAwareMatrix ( )

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broad.pda.datastructures.LocationAwareMatrix.LocationAwareMatrix	(	List< String >	rows,
		List< String >	columns,
		Map< String, LightweightGenomicAnnotation >	rowLocations
	)

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broad.pda.datastructures.LocationAwareMatrix.LocationAwareMatrix	(	BufferedReader	br,
		String	chr
	)		throws IOException, ParseException

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broad.pda.datastructures.LocationAwareMatrix.LocationAwareMatrix	(	List<?extends LightweightGenomicAnnotation >	probeData,
		List< String >	samples
	)

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broad.pda.datastructures.LocationAwareMatrix.LocationAwareMatrix ( MatrixWithHeaders mwh )

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Member Function Documentation

void broad.pda.datastructures.LocationAwareMatrix.annotation ( GenomicAnnotation annotation )

Implements broad.core.annotation.AnnotationHandler.

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void broad.pda.datastructures.LocationAwareMatrix.appendRows ( LocationAwareMatrix other )

void broad.pda.datastructures.LocationAwareMatrix.begin ( )

Implements broad.core.annotation.AnnotationHandler.

void broad.pda.datastructures.LocationAwareMatrix.browserLine ( String line )

Implements broad.core.annotation.AnnotationHandler.

void broad.pda.datastructures.LocationAwareMatrix.eof ( )

Implements broad.core.annotation.AnnotationHandler.

Set<String> broad.pda.datastructures.LocationAwareMatrix.getChromosomes ( )

LightweightGenomicAnnotation broad.pda.datastructures.LocationAwareMatrix.getClosest ( LightweightGenomicAnnotation annotation )

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LightweightGenomicAnnotation broad.pda.datastructures.LocationAwareMatrix.getNextClosest ( LightweightGenomicAnnotation annotation )

Return

Parameters

annotation

Returns: the annotation corresponding to the row that is after the given annotation in chromosome order

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List<LightweightGenomicAnnotation> broad.pda.datastructures.LocationAwareMatrix.getOverlappers ( LightweightGenomicAnnotation annotation )

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LightweightGenomicAnnotation broad.pda.datastructures.LocationAwareMatrix.getPriorClosest ( LightweightGenomicAnnotation annotation )

Parameters

annotation

Returns: the annotation corresponding to the row that is before in chromosome order

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Collection<LightweightGenomicAnnotation> broad.pda.datastructures.LocationAwareMatrix.getRowAnnotations ( )

Map<String, LightweightGenomicAnnotation> broad.pda.datastructures.LocationAwareMatrix.getRowLocationMap ( )

LightweightGenomicAnnotation broad.pda.datastructures.LocationAwareMatrix.getRowPosition ( String row )

IntervalTree<String> broad.pda.datastructures.LocationAwareMatrix.getRowTree ( String chromosome )

void broad.pda.datastructures.LocationAwareMatrix.initFromIGVMatrix	(	BufferedReader	br,
		String	header,
		String	chromosomeToLoad
	)		throws IOException, ParseException

protected

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LocationAwareMatrix broad.pda.datastructures.LocationAwareMatrix.removeOverlappingRows ( LocationAwareMatrix other )

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void broad.pda.datastructures.LocationAwareMatrix.setColumns ( List< String > columns )

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void broad.pda.datastructures.LocationAwareMatrix.setDataDimensions	(	int	rowDim,
		int	columnDim
	)

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LocationAwareMatrix broad.pda.datastructures.LocationAwareMatrix.submatrixByColumns ( Collection< String > columnNames )

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LocationAwareMatrix broad.pda.datastructures.LocationAwareMatrix.submatrixByColumns ( String[] columnNames )

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void broad.pda.datastructures.LocationAwareMatrix.track ( String line )

Implements broad.core.annotation.AnnotationHandler.

void broad.pda.datastructures.LocationAwareMatrix.write ( BufferedWriter bw ) throws IOException

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

java/broad/pda/datastructures/LocationAwareMatrix.java

Public Member Functions

Protected Member Functions

Constructor & Destructor Documentation

Member Function Documentation