umms.core.model.score.PoissonEnrichmentScore Class Reference

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

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

Classes
class	Processor

Public Member Functions
	PoissonEnrichmentScore (AlignmentModel sample, AlignmentModel ctrl, Annotation a)
	PoissonEnrichmentScore (AlignmentModel sample, Annotation a)
double	calculatePVal (double a, double b, double lambdaSample, double lambdaCtrl, double w)
double	getAverageCoverage (AlignmentModel data, CoordinateSpace coordSpace)
void	setPvalue (double scanPvalue)
double	getPvalue ()
void	setGlobalLength (double d)
void	setRegionLength (double regionLength)
double	getGlobalLength ()
double	getRegionLength ()
double	getSampleLambda ()
double	getCtrlLambda ()
double	getLocalSampleLambda ()
double	getCtrlSampleLambda ()
void	setSampleCount (double d)
void	setCtrlCount (double d)
void	setSampleTotal (double d)
void	setCtrlTotal (double d)
void	setSampleRegionTotal (double d)
void	setCtrlRegionTotal (double d)
double	getSampleCount ()
double	getCtrlCount ()
double	getSampleTotal ()
double	getCtrlTotal ()
double	getSampleRegionTotal ()
double	getCtrlRegionTotal ()
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	DEFAULT_REGION_TOTAL = -1.0
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

Detailed Description

Author

shari This class represents Poisson enrichment score for ChIP/CLIP from Mikkelsen et al. 2010. Can take either sample and control models or just sample.

Constructor & Destructor Documentation

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

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

Member Function Documentation

double umms.core.model.score.PoissonEnrichmentScore.calculatePVal	(	double	a,
		double	b,
		double	lambdaSample,
		double	lambdaCtrl,
		double	w
	)

Parameters

a	Sample reads
b	Control reads
lambdaSample	Sample reads total / Genome size (ie expected reads per base)
lambdaCtrl	Control reads total / Genome size (ie expected reads per base)
w	window size

Returns

Poisson pvalue

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double umms.core.model.score.PoissonEnrichmentScore.getAverageCoverage	(	AlignmentModel	data,
		CoordinateSpace	coordSpace
	)

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double umms.core.model.score.PoissonEnrichmentScore.getCtrlCount

(

)

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double umms.core.model.score.PoissonEnrichmentScore.getCtrlLambda

(

)

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double umms.core.model.score.PoissonEnrichmentScore.getCtrlRegionTotal

(

)

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double umms.core.model.score.PoissonEnrichmentScore.getCtrlSampleLambda

(

)

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double umms.core.model.score.PoissonEnrichmentScore.getCtrlTotal

(

)

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double umms.core.model.score.PoissonEnrichmentScore.getGlobalLength

(

)

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double umms.core.model.score.PoissonEnrichmentScore.getLocalSampleLambda

(

)

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double umms.core.model.score.PoissonEnrichmentScore.getPvalue

(

)

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double umms.core.model.score.PoissonEnrichmentScore.getRegionLength

(

)

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double umms.core.model.score.PoissonEnrichmentScore.getSampleCount

(

)

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double umms.core.model.score.PoissonEnrichmentScore.getSampleLambda

(

)

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double umms.core.model.score.PoissonEnrichmentScore.getSampleRegionTotal

(

)

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double umms.core.model.score.PoissonEnrichmentScore.getSampleTotal

(

)

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void umms.core.model.score.PoissonEnrichmentScore.setCtrlCount

(

double

d

)

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void umms.core.model.score.PoissonEnrichmentScore.setCtrlRegionTotal

(

double

d

)

void umms.core.model.score.PoissonEnrichmentScore.setCtrlTotal

(

double

d

)

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void umms.core.model.score.PoissonEnrichmentScore.setGlobalLength

(

double

d

)

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void umms.core.model.score.PoissonEnrichmentScore.setPvalue

(

double

scanPvalue

)

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void umms.core.model.score.PoissonEnrichmentScore.setRegionLength

(

double

regionLength

)

void umms.core.model.score.PoissonEnrichmentScore.setSampleCount

(

double

d

)

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void umms.core.model.score.PoissonEnrichmentScore.setSampleRegionTotal

(

double

d

)

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void umms.core.model.score.PoissonEnrichmentScore.setSampleTotal

(

double

d

)

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Member Data Documentation

double umms.core.model.score.PoissonEnrichmentScore.DEFAULT_REGION_TOTAL = -1.0

static

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

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