broad.pda.seq.rap.SkellamScore Class Reference

Inheritance diagram for broad.pda.seq.rap.SkellamScore:

Collaboration diagram for broad.pda.seq.rap.SkellamScore:

Classes
class	Processor

Public Member Functions
	SkellamScore (Annotation a)
	SkellamScore (AlignmentModel numerator, AlignmentModel denominator, Annotation annotation, double rapLambda, double backgroundLambda)
double	getScore ()
double	getNumeratorScanPVal ()
double	getDenominatorScanPVal ()
String	toString ()
double	getSkellamPValue ()
boolean	countLessThanLambda ()

Constructor & Destructor Documentation

broad.pda.seq.rap.SkellamScore.SkellamScore

(

Annotation

a

)

broad.pda.seq.rap.SkellamScore.SkellamScore	(	AlignmentModel	numerator,
		AlignmentModel	denominator,
		Annotation	annotation,
		double	rapLambda,
		double	backgroundLambda
	)

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Member Function Documentation

boolean broad.pda.seq.rap.SkellamScore.countLessThanLambda

(

)

Returns true if the signal count is less than the chromosome lambda

Returns

double broad.pda.seq.rap.SkellamScore.getDenominatorScanPVal

(

)

double broad.pda.seq.rap.SkellamScore.getNumeratorScanPVal

(

)

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double broad.pda.seq.rap.SkellamScore.getScore

(

)

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double broad.pda.seq.rap.SkellamScore.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

Returns

The probability under the null hypothesis of observing a greater difference

Exceptions

IOException

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String broad.pda.seq.rap.SkellamScore.toString

(

)

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

• java/broad/pda/seq/rap/SkellamScore.java