broad.core.motif.PositionWeightMatrix Class Reference

Inheritance diagram for broad.core.motif.PositionWeightMatrix:

Collaboration diagram for broad.core.motif.PositionWeightMatrix:

Public Member Functions
	PositionWeightMatrix (String name)
void	setMatrixFromRawData (List< String[]> unparsedRows) throws ParseException
void	setMatrix (List< double[]> sites) throws ParseException
void	addColumn (double[] site)
void	setUnparsedRow (int colNum, String[] unparsedRow) throws ParseException
void	write (BufferedWriter bw, NumberFormat formatter) throws IOException
void	writeUNIPROBE (BufferedWriter bw, NumberFormat formatter) throws IOException
String	getName ()
void	setName (String name)
int	getLeftHighInfoStart ()
int	getRightHighInfoStart ()
void	setAlignPos (int minAlignNum)
PositionWeightMatrix	trimByInformationContent (double ic)
List< Double >	computeScoreDistribution (float backgroundA, float backgroundC, float backgroundG, float backgroundT, int sampleSize)
String	printKmer (int[] kmer)
double	getLogLikelihood (char[] s)
double	getLogLikelihood (int[] s)
double	getLogLikelihood (short[] encodedSequence, int i)
int	getNumCol ()
boolean	isEmpty ()
PositionWeightMatrix	permuteColumns (boolean preserveGCDinucleotides)
PositionWeightMatrix	copy ()
double	ic ()
PositionWeightMatrix	reverseComplement ()
int	getNumEndPosToErase (double infoThreshold)
int	getNumStartPosToErase (double infoThreshold)
void	printRefinedWeightMatrix (double infoThreshold)
void	flatWeightMatrix (double infoTh)
String	getConsensus ()
boolean	getAlignDir ()
List< BED >	match (SequenceRegion region, double[] background, float minScore)
PositionWeightMatrix	createIsoPWM (double[] column, String name)
void	addPseudoCounts ()
PositionWeightMatrix	centroidOf (Collection< PositionWeightMatrix > pwmSet) throws IllegalArgumentException
double	distanceFrom (PositionWeightMatrix other)
double	kullbackLeiber (PositionWeightMatrix other)

Static Public Member Functions
static int[]	getNextKmer (int[] kmer)

Protected Member Functions
void	addToCentroid (Matrix m, PositionWeightMatrix pwm)

Constructor & Destructor Documentation

broad.core.motif.PositionWeightMatrix.PositionWeightMatrix

(

String

name

)

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Member Function Documentation

void broad.core.motif.PositionWeightMatrix.addColumn

(

double[]

site

)

void broad.core.motif.PositionWeightMatrix.addPseudoCounts

(

)

void broad.core.motif.PositionWeightMatrix.addToCentroid ( Matrix  m, PositionWeightMatrix  pwm  )

protected

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PositionWeightMatrix broad.core.motif.PositionWeightMatrix.centroidOf

(

Collection< PositionWeightMatrix >

pwmSet

)

throws IllegalArgumentException

Computes the euclidean centroid, it may not be the formal centroid for different metrics but intuitively the average counts should provide a good cluster representative which is what this method intends to return

Parameters

pwmSet

- Collection of pwms from which to compute the centroid0

Returns

The euclidean centroid

Exceptions

IllegalArgumentException

- When not all PWMs have the same dimension.

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List<Double> broad.core.motif.PositionWeightMatrix.computeScoreDistribution	(	float	backgroundA,
		float	backgroundC,
		float	backgroundG,
		float	backgroundT,
		int	sampleSize
	)

Compute Distribution of scores for motif.

Parameters

s
isNumSeq

Returns

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PositionWeightMatrix broad.core.motif.PositionWeightMatrix.copy

(

)

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PositionWeightMatrix broad.core.motif.PositionWeightMatrix.createIsoPWM	(	double[]	column,
		String	name
	)

Creates a PWM of similar dimension to this PWM but with all columns set to the given vector, usually a neutral mutation vector.

Parameters

column

Returns

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double broad.core.motif.PositionWeightMatrix.distanceFrom

(

PositionWeightMatrix

other

)

Distance between two PWMs, uses the KL similarity

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void broad.core.motif.PositionWeightMatrix.flatWeightMatrix

(

double

infoTh

)

boolean broad.core.motif.PositionWeightMatrix.getAlignDir

(

)

String broad.core.motif.PositionWeightMatrix.getConsensus

(

)

int broad.core.motif.PositionWeightMatrix.getLeftHighInfoStart

(

)

double broad.core.motif.PositionWeightMatrix.getLogLikelihood

(

char[]

s

)

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double broad.core.motif.PositionWeightMatrix.getLogLikelihood

(

int[]

s

)

double broad.core.motif.PositionWeightMatrix.getLogLikelihood	(	short[]	encodedSequence,
		int	i
	)

String broad.core.motif.PositionWeightMatrix.getName

(

)

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static int [] broad.core.motif.PositionWeightMatrix.getNextKmer ( int[]  kmer )

static

Gets the next logical kmer. If k = 4 the first 5 4mers would be: (0,0,0,0), (0,0,0,1), (0,0,0,2), (0,0,0,3), (0,0,1,0).

Parameters

kmer	- any valid kmer

Returns

Next logical kmer.

int broad.core.motif.PositionWeightMatrix.getNumCol

(

)

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int broad.core.motif.PositionWeightMatrix.getNumEndPosToErase

(

double

infoThreshold

)

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int broad.core.motif.PositionWeightMatrix.getNumStartPosToErase

(

double

infoThreshold

)

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int broad.core.motif.PositionWeightMatrix.getRightHighInfoStart

(

)

double broad.core.motif.PositionWeightMatrix.ic

(

)

Computes the information content of this position weith matris

Returns

boolean broad.core.motif.PositionWeightMatrix.isEmpty

(

)

double broad.core.motif.PositionWeightMatrix.kullbackLeiber

(

PositionWeightMatrix

other

)

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List<BED> broad.core.motif.PositionWeightMatrix.match	(	SequenceRegion	region,
		double[]	background,
		float	minScore
	)

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PositionWeightMatrix broad.core.motif.PositionWeightMatrix.permuteColumns

(

boolean

preserveGCDinucleotides

)

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String broad.core.motif.PositionWeightMatrix.printKmer

(

int[]

kmer

)

void broad.core.motif.PositionWeightMatrix.printRefinedWeightMatrix

(

double

infoThreshold

)

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PositionWeightMatrix broad.core.motif.PositionWeightMatrix.reverseComplement

(

)

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void broad.core.motif.PositionWeightMatrix.setAlignPos

(

int

minAlignNum

)

void broad.core.motif.PositionWeightMatrix.setMatrix

(

List< double[]>

sites

)

throws ParseException

void broad.core.motif.PositionWeightMatrix.setMatrixFromRawData

(

List< String[]>

unparsedRows

)

throws ParseException

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void broad.core.motif.PositionWeightMatrix.setName

(

String

name

)

void broad.core.motif.PositionWeightMatrix.setUnparsedRow	(	int	colNum,
		String[]	unparsedRow
	)		throws ParseException

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PositionWeightMatrix broad.core.motif.PositionWeightMatrix.trimByInformationContent

(

double

ic

)

Trims this PWM by removing start end ending columns with information content lesser than given.

Parameters

ic	- Columns below this ic at PWM edges will be trimmed.

Returns

The resulting PWM.

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void broad.core.motif.PositionWeightMatrix.write	(	BufferedWriter	bw,
		NumberFormat	formatter
	)		throws IOException

void broad.core.motif.PositionWeightMatrix.writeUNIPROBE	(	BufferedWriter	bw,
		NumberFormat	formatter
	)		throws IOException

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

• java/broad/core/motif/PositionWeightMatrix.java