umms.core.model.score.BinomialEnrichmentScore Class Reference

Inheritance diagram for umms.core.model.score.BinomialEnrichmentScore:

Collaboration diagram for umms.core.model.score.BinomialEnrichmentScore:

Classes
class	Processor

Public Member Functions
	BinomialEnrichmentScore (AlignmentModel sample, AlignmentModel ctrl, Annotation a, boolean fullyContained)
	BinomialEnrichmentScore (AlignmentModel sample, AlignmentModel ctrl, Annotation a, double regionLength, boolean fullyContained)
	BinomialEnrichmentScore (AlignmentModel sample, AlignmentModel ctrl, Annotation a, double regionLength)
	BinomialEnrichmentScore (AlignmentModel sample, Annotation a)
	BinomialEnrichmentScore (AlignmentModel sample, AlignmentModel ctrl, Annotation a)
	BinomialEnrichmentScore (AlignmentModel sample, AlignmentModel ctrl, Annotation a, double sampleRegCount, double ctrlRegCount)
	BinomialEnrichmentScore (AlignmentModel sample, AlignmentModel ctrl, Annotation a, double sampleRegCount, double ctrlRegCount, boolean fullyContained)
	BinomialEnrichmentScore (AlignmentModel sample, AlignmentModel ctrl, Annotation annotation, BinomialEnrichmentScore previousScore, double newSampleCount, double newCtrlCount)
	BinomialEnrichmentScore (MultiScore other)
double	calculatePVal (double a, double b, double sampleRegionCounts, double ctrlRegionCounts)
double	calculatePVal (double a, double b, double sampleRegionCounts, double ctrlRegionCounts, double regionLength, double windowSize)
void	refreshPvalue ()
double	getEnrichmentOverControl ()
void	setPvalue (double scanPvalue)
double	getPvalue ()
void	setSampleCount (double d)
void	setCtrlCount (double d)
void	setSampleRegionCount (double d)
void	setCtrlRegionCount (double d)
double	getSampleCount ()
double	getCtrlCount ()
double	getCtrlRegionCount ()
double	getSampleRegionCount ()
void	setRegionLength (double d)
double	getRegionLength ()
Public Member Functions inherited from umms.core.model.score.CountScore
	CountScore (Annotation a)
	CountScore (CountScore other)
	CountScore (CountScore other, Annotation newAnnotation, double newCount)
	CountScore (AnnotationCollection<?extends Annotation > model, Annotation annotation)
	CountScore (AnnotationCollection<?extends Annotation > model, Annotation annotation, double regionTotal)
	CountScore (AnnotationCollection<?extends Annotation > model, Annotation annotation, boolean fullyContained)
	CountScore (AnnotationCollection<?extends Annotation > model, Annotation annotation, double regionTotal, boolean fullyContained)
	CountScore (Annotation annotation, double count, double regionTotal, double total)
double	getCount ()
double	getScore ()
double	getTotal ()
double	getRegionTotal ()
double	getRPKM ()
double	getRPK ()
void	setCount (double count)
void	setTotal (double total)
void	setRegionTotal (double regionTotal)
String	toString ()
boolean	equals (Object o)
int	compareTo (CountScore o)
int	hashCode ()
void	refreshPvalue ()
double	getPvalue ()
Public Member Functions inherited from umms.core.model.score.WindowScore.AbstractWindowScore
	AbstractWindowScore (Annotation t)
Annotation	getAnnotation ()

Additional Inherited Members
Static Public Member Functions inherited from umms.core.model.score.CountScore
static double	asRPKM (double count, double total, int windowSize)
Static Public Attributes inherited from umms.core.model.score.CountScore
static double	DEFAULT_REGION_TOTAL = -1.0
Protected Attributes inherited from umms.core.model.score.WindowScore.AbstractWindowScore
Annotation	annotation

Constructor & Destructor Documentation

umms.core.model.score.BinomialEnrichmentScore.BinomialEnrichmentScore	(	AlignmentModel	sample,
		AlignmentModel	ctrl,
		Annotation	a,
		boolean	fullyContained
	)

Binomial score for windows P-Value statistics are stored here "Region" refers to an arbitrary region being scanned, like a gene, or a chromosome, or some subset of the whole coordinate space

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umms.core.model.score.BinomialEnrichmentScore.BinomialEnrichmentScore	(	AlignmentModel	sample,
		AlignmentModel	ctrl,
		Annotation	a,
		double	regionLength,
		boolean	fullyContained
	)

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umms.core.model.score.BinomialEnrichmentScore.BinomialEnrichmentScore	(	AlignmentModel	sample,
		AlignmentModel	ctrl,
		Annotation	a,
		double	regionLength
	)

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umms.core.model.score.BinomialEnrichmentScore.BinomialEnrichmentScore	(	AlignmentModel	sample,
		Annotation	a
	)

umms.core.model.score.BinomialEnrichmentScore.BinomialEnrichmentScore	(	AlignmentModel	sample,
		AlignmentModel	ctrl,
		Annotation	a
	)

umms.core.model.score.BinomialEnrichmentScore.BinomialEnrichmentScore	(	AlignmentModel	sample,
		AlignmentModel	ctrl,
		Annotation	a,
		double	sampleRegCount,
		double	ctrlRegCount
	)

umms.core.model.score.BinomialEnrichmentScore.BinomialEnrichmentScore	(	AlignmentModel	sample,
		AlignmentModel	ctrl,
		Annotation	a,
		double	sampleRegCount,
		double	ctrlRegCount,
		boolean	fullyContained
	)

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umms.core.model.score.BinomialEnrichmentScore.BinomialEnrichmentScore	(	AlignmentModel	sample,
		AlignmentModel	ctrl,
		Annotation	annotation,
		BinomialEnrichmentScore	previousScore,
		double	newSampleCount,
		double	newCtrlCount
	)

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umms.core.model.score.BinomialEnrichmentScore.BinomialEnrichmentScore

(

MultiScore

other

)

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Member Function Documentation

double umms.core.model.score.BinomialEnrichmentScore.calculatePVal	(	double	a,
		double	b,
		double	sampleRegionCounts,
		double	ctrlRegionCounts
	)

Parameters

a	Sample reads
b	Control reads
sampleRegionCounts	Sample reads in region
ctrlRegionCounts	Control reads in region

Returns

Binomial P(X>a)

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double umms.core.model.score.BinomialEnrichmentScore.calculatePVal	(	double	a,
		double	b,
		double	sampleRegionCounts,
		double	ctrlRegionCounts,
		double	regionLength,
		double	windowSize
	)

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double umms.core.model.score.BinomialEnrichmentScore.getCtrlCount

(

)

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double umms.core.model.score.BinomialEnrichmentScore.getCtrlRegionCount

(

)

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double umms.core.model.score.BinomialEnrichmentScore.getEnrichmentOverControl

(

)

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double umms.core.model.score.BinomialEnrichmentScore.getPvalue

(

)

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double umms.core.model.score.BinomialEnrichmentScore.getRegionLength

(

)

double umms.core.model.score.BinomialEnrichmentScore.getSampleCount

(

)

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double umms.core.model.score.BinomialEnrichmentScore.getSampleRegionCount

(

)

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void umms.core.model.score.BinomialEnrichmentScore.refreshPvalue

(

)

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void umms.core.model.score.BinomialEnrichmentScore.setCtrlCount

(

double

d

)

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void umms.core.model.score.BinomialEnrichmentScore.setCtrlRegionCount

(

double

d

)

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void umms.core.model.score.BinomialEnrichmentScore.setPvalue

(

double

scanPvalue

)

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void umms.core.model.score.BinomialEnrichmentScore.setRegionLength

(

double

d

)

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void umms.core.model.score.BinomialEnrichmentScore.setSampleCount

(

double

d

)

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void umms.core.model.score.BinomialEnrichmentScore.setSampleRegionCount

(

double

d

)

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

• java/umms/core/model/score/BinomialEnrichmentScore.java