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

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

Classes
class	Processor

class	RatioScoreIterator

Public Member Functions
	RatioScore (Annotation a)

	RatioScore (Annotation numerator, Annotation denominator, double nTotal, double dTotal)

	RatioScore (Annotation numerator, Annotation denominator, double nTotal, double dTotal, double nRegionTotal, double dRegionTotal)

	RatioScore (CountScore numerator, CountScore denominator)

	RatioScore (AnnotationCollection<?extends Annotation > numerator, AnnotationCollection<?extends Annotation > denominator, Annotation annotation)

	RatioScore (AnnotationCollection<?extends Annotation > numerator, AnnotationCollection<?extends Annotation > denominator, Annotation annotation, double numeratorRegionTotal, double denominatorRegionTotal)

void	setNumeratorCount (double d)

void	setDenominatorCount (double d)

void	setNumeratorTotal (double d)

void	setDenominatorTotal (double d)

void	setNumeratorRegionTotal (double d)

void	setDenominatorRegionTotal (double d)

double	getNumeratorCount ()

double	getDenominatorCount ()

double	getNumeratorTotal ()

double	getDenominatorTotal ()

double	getNumeratorRegionTotal ()

double	getDenominatorRegionTotal ()

double	getNumeratorRPKM ()

double	getDenominatorRPKM ()

double	getRatio ()

double	getScore ()

double	getEnrichmentBinomialScore ()

double	getEnrichmentBinomialPValue ()

double	getDepletionBinomialScore ()

double	getDepletionBinomialPValue ()

double	getLog2Ratio ()

double	getRegionRatio ()

double	getLog2RegionRatio ()

double	getRegionNumeratorRPKM ()

double	getRegionDenominatorRPKM ()

String	toString ()

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 ()

Static Public Attributes
static double	RPKM_OFFSET = 0.001

Static Public Attributes inherited from umms.core.model.score.CountScore
static double	DEFAULT_REGION_TOTAL = -1.0

Additional Inherited Members
Static Public Member Functions inherited from umms.core.model.score.CountScore
static double	asRPKM (double count, double total, int windowSize)

Protected Attributes inherited from umms.core.model.score.WindowScore.AbstractWindowScore
Annotation	annotation

Constructor & Destructor Documentation

umms.core.model.score.RatioScore.RatioScore ( Annotation a )

umms.core.model.score.RatioScore.RatioScore	(	Annotation	numerator,
		Annotation	denominator,
		double	nTotal,
		double	dTotal
	)

umms.core.model.score.RatioScore.RatioScore	(	Annotation	numerator,
		Annotation	denominator,
		double	nTotal,
		double	dTotal,
		double	nRegionTotal,
		double	dRegionTotal
	)

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umms.core.model.score.RatioScore.RatioScore	(	CountScore	numerator,
		CountScore	denominator
	)

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umms.core.model.score.RatioScore.RatioScore	(	AnnotationCollection<?extends Annotation >	numerator,
		AnnotationCollection<?extends Annotation >	denominator,
		Annotation	annotation
	)

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umms.core.model.score.RatioScore.RatioScore	(	AnnotationCollection<?extends Annotation >	numerator,
		AnnotationCollection<?extends Annotation >	denominator,
		Annotation	annotation,
		double	numeratorRegionTotal,
		double	denominatorRegionTotal
	)

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Member Function Documentation

double umms.core.model.score.RatioScore.getDenominatorCount ( )

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double umms.core.model.score.RatioScore.getDenominatorRegionTotal ( )

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double umms.core.model.score.RatioScore.getDenominatorRPKM ( )

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double umms.core.model.score.RatioScore.getDenominatorTotal ( )

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double umms.core.model.score.RatioScore.getDepletionBinomialPValue ( )

Binomial test: combine numerator and denominator counts, then calculate cumulative probability of seeing less than this proportion

Returns: p-value for the numerator having less reads than expected.

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double umms.core.model.score.RatioScore.getDepletionBinomialScore ( )

Binomial test: combine numerator and denominator counts, then calculate cumulative probability of seeing less than this proportion

Returns: -log10 p-value for the numerator having less reads than expected.

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double umms.core.model.score.RatioScore.getEnrichmentBinomialPValue ( )

Binomial test: combine numerator and denominator counts, then calculate cumulative probability of seeing >= this proportion

Returns: p-value for the numerator having more reads than expected

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double umms.core.model.score.RatioScore.getEnrichmentBinomialScore ( )

Binomial test: combine numerator and denominator counts, then calculate cumulative probability of seeing >= this proportion

Returns: -log10 p-value for the numerator having more reads than expected.

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double umms.core.model.score.RatioScore.getLog2Ratio ( )

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double umms.core.model.score.RatioScore.getLog2RegionRatio ( )

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double umms.core.model.score.RatioScore.getNumeratorCount ( )

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double umms.core.model.score.RatioScore.getNumeratorRegionTotal ( )

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double umms.core.model.score.RatioScore.getNumeratorRPKM ( )

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double umms.core.model.score.RatioScore.getNumeratorTotal ( )

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double umms.core.model.score.RatioScore.getRatio ( )

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double umms.core.model.score.RatioScore.getRegionDenominatorRPKM ( )

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double umms.core.model.score.RatioScore.getRegionNumeratorRPKM ( )

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double umms.core.model.score.RatioScore.getRegionRatio ( )

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double umms.core.model.score.RatioScore.getScore ( )

Returns the number of reads overlapping this region

Returns: number of reds overlapping this window Returns the "score" as defined by each subclass (e.g. count, ratio, sum of annotation scores, etc.)

Implements umms.core.model.score.WindowScore.

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