broad.pda.seq.segmentation.AlignmentDataModelStats Class Reference

Classes
class	ReadCountNormalizerToBaselineAlignment

Public Member Functions
	AlignmentDataModelStats ()
	AlignmentDataModelStats (AlignmentDataModel data, Map< String, Integer > maskedRegions, String chr) throws IOException
	AlignmentDataModelStats (AlignmentDataModel data, Map< String, Integer > maskedRegions, String chr, double lambda, boolean loadChromosomeStats) throws IOException
	AlignmentDataModelStats (AlignmentDataModel data, Map< String, Integer > maskedRegions) throws IOException
	AlignmentDataModelStats (AlignmentDataModel data, Map< String, Integer > maskedRegions, Map< String, Double > readsPerChromosome) throws IOException
	AlignmentDataModelStats (AlignmentDataModel data, Map< String, Integer > maskedRegions, String chr, boolean loadChromosomeStats) throws IOException
	AlignmentDataModelStats (AlignmentDataModel data, Map< String, Integer > maskedRegions, double lambda) throws IOException
	AlignmentDataModelStats (AlignmentDataModel data, Map< String, Integer > maskedRegions, double lambda, boolean loadChromosomeStats) throws IOException
	AlignmentDataModelStats (AlignmentDataModel data, Map< String, Integer > maskedRegions, String chr, double lambda) throws IOException
	AlignmentDataModelStats (AlignmentDataModel data, String chr) throws IOException
	AlignmentDataModelStats (AlignmentDataModel data) throws IOException
void	init (Map< String, Integer > maskedRegions, double lambda, boolean loadChromosomeStats) throws IOException
void	init (Map< String, Integer > maskedRegions, double lambda, boolean loadChromosomeStats, Map< String, Double > readsByChr) throws IOException
AlignmentDataModel	getData ()
double	getGlobalRPKMConstant ()
Map< String, Double >	getNumberOfReads ()
double	getLambda (String chr) throws IOException
double	getSum (String chr) throws IOException
double	getNumberOfReads (String chr) throws IOException
double	getNumberOfReadsByChr (String chr) throws IOException
int	getTotalReads () throws IOException
double	getNumberMarkers (String chr) throws IOException
Map< String, Integer >	getChromosomeLengths ()
int[]	getGeneCounts (Collection< Gene > genes, int extensionFactor) throws IOException
int[]	getGeneCountsWithoutDatasetTotals (Collection< Gene > genes, int extensionFactor) throws IOException
Map< Gene, double[]>	getGeneExpression (Collection< Gene > genes, int extensionFactor) throws IOException
int	getCounts (Collection< Annotation > Annotation, int extensionFactor) throws IOException
double	getCountsPerAlignment (Annotation align, IntervalTree< Alignment > tree, int extensionFactor)
double	getCountsPerAlignment (Gene window, IntervalTree< Alignment > tree, int extensionFactor)
double	getCountsPerAlignment (Annotation align, Map< String, IntervalTree< Annotation >> exonTree, IntervalTree< Alignment > tree, int extensionFactor)
double	getRPKMConstant (String chr)
Map< Annotation, Integer >	getSplicedReads (Annotation chrRegion, int i, int j) throws IOException
Map< Annotation, Integer >	getSplicedReads (Annotation region, List< Predicate< Annotation >> filters, int minNumIntrons) throws IOException
Map< Annotation, Integer >	getSplicedReads (Annotation region, int minIntronSize, int maxIntronSize, int minNumberOfSplices, Sequence chrSequence) throws IOException
IntervalTree< Alignment >	getIntervalTree (LightweightGenomicAnnotation region) throws IOException
IntervalTree< Alignment >	getIntervalTree (String chr, int start, int end) throws IOException
IntervalTree< Alignment >	getIntervalTreeCached (String chr, int start, int end) throws IOException
IntervalTree< Alignment >	getIntervalTreeTruncatedCached (String chromosome, int start, int end) throws IOException
double	getScorePerAlignmentFromCache (Gene window, IntervalTree< Alignment > chunkAlignmentTree, int extensionFactor)
int	getChunkStart ()
int	getChunkEnd ()
double	getSpliceWeightFactor ()
Iterator< Annotation >	getExonAnnotationOverlappingRegion (Annotation align) throws IOException
CloseableIterator< Alignment >	getAnnotationOverlappingRegion (Annotation Annotation) throws IOException
double	getCountsOfUniqueOverlappers (Annotation startPosition, Annotation window, IntervalTree< Alignment > chunkAlignmentTree, int extensionFactor)
CloseableIterator< Alignment >	getReadIterator ()
CloseableIterator< Alignment >	getReadIterator (Annotation region) throws IOException
double	getMinimumMappingQuality ()
void	setAlignmentDataModel (AlignmentDataModel data)
void	setCountNormalizer (ReadCountNormalizer normalizer)
void	setLambda (String chr, double numberOfReads)
void	setNumberOfReads (String chr, double numberOfReads2)
void	setMinimumMappingQuality (double minMapQual)
void	setNumberOfMarkers (String chr, double numMarkers2)
void	setChunkSize (int chunkSize)
void	resetTreeCache ()
void	resetTreeCache (String chr)
double[]	scanPRate (Gene gene, int extensionFactor) throws IOException
double[]	scanRegion (int fixedWidth, LightweightGenomicAnnotation region) throws IOException
Gene	getPeak (Gene gene, Gene startCodon, IntervalTree< Alignment > tree, int EF)
double[]	scanPRate (LightweightGenomicAnnotation annotation, int extensionFactor) throws IOException
double[]	scanPRate (Gene gene, IntervalTree< Alignment > tree, int extensionFactor) throws IOException
double[]	scanPRate (Annotation align, IntervalTree< Alignment > tree, double localLambda, int extensionFactor) throws IOException
double[]	scanPRate (Annotation align, double readCount, int extenstionFactor) throws IOException
double[]	scanPRate (Annotation align, double readCount, double localLambda, int extenstionFactor) throws IOException
double[]	scanPRate (Gene gene, IntervalTree< Alignment > tree, double localLambda, int extensionFactor) throws IOException
double[]	scanPRate (Gene gene, IntervalTree< Alignment > tree, double localLambda, int extensionFactor, double numMarkers) throws IOException
double	count (Annotation align, int extensionFactor) throws IOException
int	countWithinExon (Annotation align, int extensionFactor) throws IOException
boolean	isPaired ()
int	chromosomeLength (String chr)
boolean	passes (Gene window, IntervalTree< Alignment > chunkAlignmentTree, int i, int critVal)
void	normalizeReadCountsToBaseModel (AlignmentDataModelStats baseline) throws IOException
double	getMaskedRegionsSize (String chr)
void	setStoredStats (StoredAlignmentStats sas)
void	setExtensionFactor (int extensionFactor)

Constructor & Destructor Documentation

broad.pda.seq.segmentation.AlignmentDataModelStats.AlignmentDataModelStats

(

)

broad.pda.seq.segmentation.AlignmentDataModelStats.AlignmentDataModelStats	(	AlignmentDataModel	data,
		Map< String, Integer >	maskedRegions,
		String	chr
	)		throws IOException

broad.pda.seq.segmentation.AlignmentDataModelStats.AlignmentDataModelStats	(	AlignmentDataModel	data,
		Map< String, Integer >	maskedRegions,
		String	chr,
		double	lambda,
		boolean	loadChromosomeStats
	)		throws IOException

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broad.pda.seq.segmentation.AlignmentDataModelStats.AlignmentDataModelStats	(	AlignmentDataModel	data,
		Map< String, Integer >	maskedRegions
	)		throws IOException

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broad.pda.seq.segmentation.AlignmentDataModelStats.AlignmentDataModelStats	(	AlignmentDataModel	data,
		Map< String, Integer >	maskedRegions,
		Map< String, Double >	readsPerChromosome
	)		throws IOException

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broad.pda.seq.segmentation.AlignmentDataModelStats.AlignmentDataModelStats	(	AlignmentDataModel	data,
		Map< String, Integer >	maskedRegions,
		String	chr,
		boolean	loadChromosomeStats
	)		throws IOException

broad.pda.seq.segmentation.AlignmentDataModelStats.AlignmentDataModelStats	(	AlignmentDataModel	data,
		Map< String, Integer >	maskedRegions,
		double	lambda
	)		throws IOException

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broad.pda.seq.segmentation.AlignmentDataModelStats.AlignmentDataModelStats	(	AlignmentDataModel	data,
		Map< String, Integer >	maskedRegions,
		double	lambda,
		boolean	loadChromosomeStats
	)		throws IOException

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broad.pda.seq.segmentation.AlignmentDataModelStats.AlignmentDataModelStats	(	AlignmentDataModel	data,
		Map< String, Integer >	maskedRegions,
		String	chr,
		double	lambda
	)		throws IOException

broad.pda.seq.segmentation.AlignmentDataModelStats.AlignmentDataModelStats	(	AlignmentDataModel	data,
		String	chr
	)		throws IOException

broad.pda.seq.segmentation.AlignmentDataModelStats.AlignmentDataModelStats

(

AlignmentDataModel

data

)

throws IOException

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Member Function Documentation

int broad.pda.seq.segmentation.AlignmentDataModelStats.chromosomeLength

(

String

chr

)

double broad.pda.seq.segmentation.AlignmentDataModelStats.count	(	Annotation	align,
		int	extensionFactor
	)		throws IOException

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int broad.pda.seq.segmentation.AlignmentDataModelStats.countWithinExon	(	Annotation	align,
		int	extensionFactor
	)		throws IOException

CloseableIterator<Alignment> broad.pda.seq.segmentation.AlignmentDataModelStats.getAnnotationOverlappingRegion

(

Annotation

Annotation

)

throws IOException

Map<String, Integer> broad.pda.seq.segmentation.AlignmentDataModelStats.getChromosomeLengths

(

)

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int broad.pda.seq.segmentation.AlignmentDataModelStats.getChunkEnd

(

)

int broad.pda.seq.segmentation.AlignmentDataModelStats.getChunkStart

(

)

int broad.pda.seq.segmentation.AlignmentDataModelStats.getCounts	(	Collection< Annotation >	Annotation,
		int	extensionFactor
	)		throws IOException

double broad.pda.seq.segmentation.AlignmentDataModelStats.getCountsOfUniqueOverlappers	(	Annotation	startPosition,
		Annotation	window,
		IntervalTree< Alignment >	chunkAlignmentTree,
		int	extensionFactor
	)

double broad.pda.seq.segmentation.AlignmentDataModelStats.getCountsPerAlignment	(	Annotation	align,
		IntervalTree< Alignment >	tree,
		int	extensionFactor
	)

double broad.pda.seq.segmentation.AlignmentDataModelStats.getCountsPerAlignment	(	Gene	window,
		IntervalTree< Alignment >	tree,
		int	extensionFactor
	)

double broad.pda.seq.segmentation.AlignmentDataModelStats.getCountsPerAlignment	(	Annotation	align,
		Map< String, IntervalTree< Annotation >>	exonTree,
		IntervalTree< Alignment >	tree,
		int	extensionFactor
	)

AlignmentDataModel broad.pda.seq.segmentation.AlignmentDataModelStats.getData

(

)

Iterator<Annotation> broad.pda.seq.segmentation.AlignmentDataModelStats.getExonAnnotationOverlappingRegion

(

Annotation

align

)

throws IOException

int [] broad.pda.seq.segmentation.AlignmentDataModelStats.getGeneCounts	(	Collection< Gene >	genes,
		int	extensionFactor
	)		throws IOException

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int [] broad.pda.seq.segmentation.AlignmentDataModelStats.getGeneCountsWithoutDatasetTotals	(	Collection< Gene >	genes,
		int	extensionFactor
	)		throws IOException

Get read counts mapping to exons, introns, 5'UTRs and 3'UTRs in gene set of interest

Parameters

genes
extensionFactor

Returns

An int array consisting of counts for exons, introns, 5'UTRs, 3'UTRs

Exceptions

IOException

Map<Gene, double[]> broad.pda.seq.segmentation.AlignmentDataModelStats.getGeneExpression	(	Collection< Gene >	genes,
		int	extensionFactor
	)		throws IOException

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double broad.pda.seq.segmentation.AlignmentDataModelStats.getGlobalRPKMConstant

(

)

IntervalTree<Alignment> broad.pda.seq.segmentation.AlignmentDataModelStats.getIntervalTree

(

LightweightGenomicAnnotation

region

)

throws IOException

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IntervalTree<Alignment> broad.pda.seq.segmentation.AlignmentDataModelStats.getIntervalTree	(	String	chr,
		int	start,
		int	end
	)		throws IOException

IntervalTree<Alignment> broad.pda.seq.segmentation.AlignmentDataModelStats.getIntervalTreeCached	(	String	chr,
		int	start,
		int	end
	)		throws IOException

IntervalTree<Alignment> broad.pda.seq.segmentation.AlignmentDataModelStats.getIntervalTreeTruncatedCached	(	String	chromosome,
		int	start,
		int	end
	)		throws IOException

double broad.pda.seq.segmentation.AlignmentDataModelStats.getLambda

(

String

chr

)

throws IOException

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double broad.pda.seq.segmentation.AlignmentDataModelStats.getMaskedRegionsSize

(

String

chr

)

double broad.pda.seq.segmentation.AlignmentDataModelStats.getMinimumMappingQuality

(

)

double broad.pda.seq.segmentation.AlignmentDataModelStats.getNumberMarkers

(

String

chr

)

throws IOException

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Map<String, Double> broad.pda.seq.segmentation.AlignmentDataModelStats.getNumberOfReads

(

)

double broad.pda.seq.segmentation.AlignmentDataModelStats.getNumberOfReads

(

String

chr

)

throws IOException

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double broad.pda.seq.segmentation.AlignmentDataModelStats.getNumberOfReadsByChr

(

String

chr

)

throws IOException

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Gene broad.pda.seq.segmentation.AlignmentDataModelStats.getPeak	(	Gene	gene,
		Gene	startCodon,
		IntervalTree< Alignment >	tree,
		int	EF
	)

CloseableIterator<Alignment> broad.pda.seq.segmentation.AlignmentDataModelStats.getReadIterator

(

)

CloseableIterator<Alignment> broad.pda.seq.segmentation.AlignmentDataModelStats.getReadIterator

(

Annotation

region

)

throws IOException

double broad.pda.seq.segmentation.AlignmentDataModelStats.getRPKMConstant

(

String

chr

)

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double broad.pda.seq.segmentation.AlignmentDataModelStats.getScorePerAlignmentFromCache	(	Gene	window,
		IntervalTree< Alignment >	chunkAlignmentTree,
		int	extensionFactor
	)

Map<Annotation, Integer> broad.pda.seq.segmentation.AlignmentDataModelStats.getSplicedReads	(	Annotation	chrRegion,
		int	i,
		int	j
	)		throws IOException

Map<Annotation, Integer> broad.pda.seq.segmentation.AlignmentDataModelStats.getSplicedReads	(	Annotation	region,
		List< Predicate< Annotation >>	filters,
		int	minNumIntrons
	)		throws IOException

Map<Annotation, Integer> broad.pda.seq.segmentation.AlignmentDataModelStats.getSplicedReads	(	Annotation	region,
		int	minIntronSize,
		int	maxIntronSize,
		int	minNumberOfSplices,
		Sequence	chrSequence
	)		throws IOException

double broad.pda.seq.segmentation.AlignmentDataModelStats.getSpliceWeightFactor

(

)

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double broad.pda.seq.segmentation.AlignmentDataModelStats.getSum

(

String

chr

)

throws IOException

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int broad.pda.seq.segmentation.AlignmentDataModelStats.getTotalReads

(

)

throws IOException

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void broad.pda.seq.segmentation.AlignmentDataModelStats.init	(	Map< String, Integer >	maskedRegions,
		double	lambda,
		boolean	loadChromosomeStats
	)		throws IOException

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void broad.pda.seq.segmentation.AlignmentDataModelStats.init	(	Map< String, Integer >	maskedRegions,
		double	lambda,
		boolean	loadChromosomeStats,
		Map< String, Double >	readsByChr
	)		throws IOException

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boolean broad.pda.seq.segmentation.AlignmentDataModelStats.isPaired

(

)

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void broad.pda.seq.segmentation.AlignmentDataModelStats.normalizeReadCountsToBaseModel

(

AlignmentDataModelStats

baseline

)

throws IOException

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boolean broad.pda.seq.segmentation.AlignmentDataModelStats.passes	(	Gene	window,
		IntervalTree< Alignment >	chunkAlignmentTree,
		int	i,
		int	critVal
	)

void broad.pda.seq.segmentation.AlignmentDataModelStats.resetTreeCache

(

)

void broad.pda.seq.segmentation.AlignmentDataModelStats.resetTreeCache

(

String

chr

)

double [] broad.pda.seq.segmentation.AlignmentDataModelStats.scanPRate	(	Gene	gene,
		int	extensionFactor
	)		throws IOException

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double [] broad.pda.seq.segmentation.AlignmentDataModelStats.scanPRate	(	LightweightGenomicAnnotation	annotation,
		int	extensionFactor
	)		throws IOException

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double [] broad.pda.seq.segmentation.AlignmentDataModelStats.scanPRate	(	Gene	gene,
		IntervalTree< Alignment >	tree,
		int	extensionFactor
	)		throws IOException

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double [] broad.pda.seq.segmentation.AlignmentDataModelStats.scanPRate	(	Annotation	align,
		IntervalTree< Alignment >	tree,
		double	localLambda,
		int	extensionFactor
	)		throws IOException

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double [] broad.pda.seq.segmentation.AlignmentDataModelStats.scanPRate	(	Annotation	align,
		double	readCount,
		int	extenstionFactor
	)		throws IOException

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double [] broad.pda.seq.segmentation.AlignmentDataModelStats.scanPRate	(	Annotation	align,
		double	readCount,
		double	localLambda,
		int	extenstionFactor
	)		throws IOException

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double [] broad.pda.seq.segmentation.AlignmentDataModelStats.scanPRate	(	Gene	gene,
		IntervalTree< Alignment >	tree,
		double	localLambda,
		int	extensionFactor
	)		throws IOException

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double [] broad.pda.seq.segmentation.AlignmentDataModelStats.scanPRate	(	Gene	gene,
		IntervalTree< Alignment >	tree,
		double	localLambda,
		int	extensionFactor,
		double	numMarkers
	)		throws IOException

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double [] broad.pda.seq.segmentation.AlignmentDataModelStats.scanRegion	(	int	fixedWidth,
		LightweightGenomicAnnotation	region
	)		throws IOException

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void broad.pda.seq.segmentation.AlignmentDataModelStats.setAlignmentDataModel

(

AlignmentDataModel

data

)

void broad.pda.seq.segmentation.AlignmentDataModelStats.setChunkSize

(

int

chunkSize

)

void broad.pda.seq.segmentation.AlignmentDataModelStats.setCountNormalizer

(

ReadCountNormalizer

normalizer

)

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void broad.pda.seq.segmentation.AlignmentDataModelStats.setExtensionFactor

(

int

extensionFactor

)

void broad.pda.seq.segmentation.AlignmentDataModelStats.setLambda	(	String	chr,
		double	numberOfReads
	)

void broad.pda.seq.segmentation.AlignmentDataModelStats.setMinimumMappingQuality

(

double

minMapQual

)

void broad.pda.seq.segmentation.AlignmentDataModelStats.setNumberOfMarkers	(	String	chr,
		double	numMarkers2
	)

void broad.pda.seq.segmentation.AlignmentDataModelStats.setNumberOfReads	(	String	chr,
		double	numberOfReads2
	)

void broad.pda.seq.segmentation.AlignmentDataModelStats.setStoredStats

(

StoredAlignmentStats

sas

)

---

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

• java/broad/pda/seq/segmentation/AlignmentDataModelStats.java