broad.core.math.PermutationDistribution Class Reference

Public Member Functions
	PermutationDistribution (Annotation parentRegion, String bamFile, String bedFile, int numPermutations) throws IOException
	PermutationDistribution (Annotation parentRegion, String bamFile, String bedFile, int numPermutations, int maxGenomicSpan) throws IOException
	PermutationDistribution (Annotation parentRegion, AlignmentModel alignments, CoordinateSpace coordinateSpace, int numPermutations)
	PermutationDistribution (Annotation parentRegion, AlignmentModel alignments, CoordinateSpace coordinateSpace, int numPermutations, int maxGenomicSpan)
double	getScanPvalue (Annotation window)
EmpiricalDistribution	getScanDistribution (int windowSize)
void	writeWigEachPosition (String outWig) throws IOException
void	writeWindowsWithPvalue (int windowSize, String outBed) throws IOException

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

Detailed Description

Author

prussell

Constructor & Destructor Documentation

broad.core.math.PermutationDistribution.PermutationDistribution	(	Annotation	parentRegion,
		String	bamFile,
		String	bedFile,
		int	numPermutations
	)		throws IOException

Parameters

parentRegion	Parent region
bamFile	Bam file
bedFile	Bed file for transcriptome space
numPermutations	Number of permutations

Exceptions

IOException

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broad.core.math.PermutationDistribution.PermutationDistribution	(	Annotation	parentRegion,
		String	bamFile,
		String	bedFile,
		int	numPermutations,
		int	maxGenomicSpan
	)		throws IOException

Parameters

parentRegion	Parent region
bamFile	Bam file
bedFile	Bed file for transcriptome space
numPermutations	Number of permutations
maxGenomicSpan	Max genomic span for paired reads

Exceptions

IOException

broad.core.math.PermutationDistribution.PermutationDistribution	(	Annotation	parentRegion,
		AlignmentModel	alignments,
		CoordinateSpace	coordinateSpace,
		int	numPermutations
	)

Parameters

parentRegion	Parent annotation
alignments	Collection of annotations to count e.g. read mappings
coordinateSpace	Coordinate space
numPermutations	Number of permutations

broad.core.math.PermutationDistribution.PermutationDistribution	(	Annotation	parentRegion,
		AlignmentModel	alignments,
		CoordinateSpace	coordinateSpace,
		int	numPermutations,
		int	maxGenomicSpan
	)

Parameters

parentRegion	Parent annotation
alignments	Collection of annotations to count e.g. read mappings
coordinateSpace	Coordinate space
numPermutations	Number of permutations
maxGenomicSpan	Max genomic span for paired reads

Member Function Documentation

EmpiricalDistribution broad.core.math.PermutationDistribution.getScanDistribution

(

int

windowSize

)

Get scan distribution for the window size

Parameters

windowSize

Window size

Returns

Scan distribution

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double broad.core.math.PermutationDistribution.getScanPvalue

(

Annotation

window

)

Get scan P value of window

Parameters

window

The window

Returns

The percentage of permutations with a window of the same size that has more overlapping fragments

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static void broad.core.math.PermutationDistribution.main ( String[]  args ) throws IOException

static

Parameters

args

Exceptions

IOException

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void broad.core.math.PermutationDistribution.writeWigEachPosition

(

String

outWig

)

throws IOException

Write a wig file of -log10(Pvalue) at each position of annotation

Parameters

outWig

Output wig file

Exceptions

IOException

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void broad.core.math.PermutationDistribution.writeWindowsWithPvalue	(	int	windowSize,
		String	outBed
	)		throws IOException

Write windows to bed file with scan P value in score field

Parameters

windowSize	Window size
outBed	Output bed file

Exceptions

IOException

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

• java/broad/core/math/PermutationDistribution.java