broad.pda.seq.rap.RAPPeakCaller Class Reference

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

Public Member Functions
	RAPPeakCaller (String backgroundFile, String rapFile, String sizes, String maskedregions, int windowSize, int step) throws IOException
void	callSkellamPeaks (String outFile, double maxSkellam, double maxScanPvalue) throws IOException
void	callKLPeaks (String outFile, double klCutOff) throws IOException
CoordinateSpace	getCoordinateSpace ()

Static Public Member Functions
static void	main (String[] args) throws IOException

Static Protected Attributes
static Logger	logger = Logger.getLogger(RAPPeakCaller.class.getName())

Detailed Description

Author

skadri

Constructor & Destructor Documentation

broad.pda.seq.rap.RAPPeakCaller.RAPPeakCaller	(	String	backgroundFile,
		String	rapFile,
		String	sizes,
		String	maskedregions,
		int	windowSize,
		int	step
	)		throws IOException

Parameters

backgroundFile	Alignment file for the input sample
rapFile	Alignment file for the rap file
sizes	Chromosome sizes
windowSize	Window Size
step	Step Size / Overlap between consecutive windows
maxSkellam
maxScanPvalue

Exceptions

IOException

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Member Function Documentation

void broad.pda.seq.rap.RAPPeakCaller.callKLPeaks	(	String	outFile,
		double	klCutOff
	)		throws IOException

For each window, calculate the poisson lambda for the given window over the entire chromosome

Parameters

model
window
windowSize

Returns

Exceptions

IOException

void broad.pda.seq.rap.RAPPeakCaller.callSkellamPeaks	(	String	outFile,
		double	maxSkellam,
		double	maxScanPvalue
	)		throws IOException

Call peaks using skellam

Parameters

outFile

Exceptions

IOException

CoordinateSpace broad.pda.seq.rap.RAPPeakCaller.getCoordinateSpace

(

)

Returns the coordinate space for this peak caller

static void broad.pda.seq.rap.RAPPeakCaller.main ( String[]  args ) throws IOException

static

Parameters

args

Exceptions

IOException

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Member Data Documentation

Logger broad.pda.seq.rap.RAPPeakCaller.logger = Logger.getLogger(RAPPeakCaller.class.getName())

staticprotected

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

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