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

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

Classes
class	Processor

Public Member Functions
	WindowAllScore (Annotation a)

	WindowAllScore (AlignmentModel numerator, AlignmentModel denominator, Annotation annotation)

	WindowAllScore (AlignmentModel numerator, AlignmentModel denominator, Annotation annotation, double numeratorRegionTotal, double denominatorRegionTotal, double rapLambda, double backgroundLambda)

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	getDenominatorLambda ()

double	getNumeratorLambda ()

double	getNumeratorRPKM ()

double	getDenominatorRPKM ()

double	getRatio ()

double	getScore ()

double	getSkellamPValue ()

void	setNumeratorScanPVal (double pval)

void	setDenominatorScanPVal (double pval)

double	getNumeratorScanPVal ()

double	getDenominatorScanPVal ()

double	getEnrichmentBinomialPValue ()

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 final 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.WindowAllScore.WindowAllScore ( Annotation a )

umms.core.model.score.WindowAllScore.WindowAllScore	(	AlignmentModel	numerator,
		AlignmentModel	denominator,
		Annotation	annotation
	)

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umms.core.model.score.WindowAllScore.WindowAllScore	(	AlignmentModel	numerator,
		AlignmentModel	denominator,
		Annotation	annotation,
		double	numeratorRegionTotal,
		double	denominatorRegionTotal,
		double	rapLambda,
		double	backgroundLambda
	)

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Member Function Documentation

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

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double umms.core.model.score.WindowAllScore.getDenominatorLambda ( )

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

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

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double umms.core.model.score.WindowAllScore.getDenominatorScanPVal ( )

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

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

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.WindowAllScore.getEnrichmentBinomialPValue ( )

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.WindowAllScore.getLog2Ratio ( )

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

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

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double umms.core.model.score.WindowAllScore.getNumeratorLambda ( )

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

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

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double umms.core.model.score.WindowAllScore.getNumeratorScanPVal ( )

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

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

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

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

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

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double umms.core.model.score.WindowAllScore.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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double umms.core.model.score.WindowAllScore.getSkellamPValue ( )

Based on prussell's function in PairedSampleCoverage Compute Skellam P-value of read counts in a region given the two parameters denominatorLambda Poisson lambda for background sample numeratorLambda Poisson lambda for signal sample denominatorCount The count for background sample numeratorCount The count for signal sample