broad.pda.seq.segmentation.ContinuousDataAlignmentModel Class Reference

Collaboration diagram for broad.pda.seq.segmentation.ContinuousDataAlignmentModel:

Public Member Functions
	ContinuousDataAlignmentModel (AlignmentDataModel data) throws IOException
	ContinuousDataAlignmentModel (AlignmentDataModelStats data) throws IOException
	ContinuousDataAlignmentModel (AlignmentDataModelStats data, int EF, int minSpliceSupport) throws IOException
	ContinuousDataAlignmentModel (AlignmentDataModelStats data, File[] maskFiles, int minSpliceSupport) throws IOException
	ContinuousDataAlignmentModel (AlignmentDataModelStats data, File[] maskFiles, int EF, int minSpliceSupport, AlignmentDataModelStats pairedData, AlignmentDataModelStats strandSpecificReads) throws IOException
	ContinuousDataAlignmentModel (AlignmentDataModelStats data, File[] maskFiles, int EF, int minSpliceSupport, AlignmentDataModelStats pairedData, AlignmentDataModelStats strandSpecificReads, boolean upweight) throws IOException
	ContinuousDataAlignmentModel (AlignmentDataModelStats data, Map< String, Integer > maskFileData, int EF, int minSpliceSupport, AlignmentDataModelStats pairedData, AlignmentDataModelStats strandSpecificReads) throws IOException
	ContinuousDataAlignmentModel (AlignmentDataModelStats data, Map< String, Integer > maskFileData, int EF, int minSpliceSupport, AlignmentDataModelStats pairedData, AlignmentDataModelStats strandSpecificReads, boolean upWeight) throws IOException
	ContinuousDataAlignmentModel (AlignmentDataModelStats data, Map< String, Integer > maskFileData, int EF, int minSpliceSupport, AlignmentDataModelStats pairedData, AlignmentDataModelStats strandSpecificReads, int chunkSize, boolean upWeightSplices) throws IOException
	ContinuousDataAlignmentModel (AlignmentDataModelStats data, File[] maskFiles, int EF, int minSpliceSupport, AlignmentDataModelStats pairedData) throws IOException
	ContinuousDataAlignmentModel (AlignmentDataModelStats data, File[] maskFiles, int EF, int minSpliceSupport) throws IOException
void	setFindMaxContiguous (boolean findMaxContiguous)
void	setTrimEnds (boolean trimEnds)
void	setMinContguousSegmentSize (int minSize)
void	setAlpha (double alpha)
void	setUpWeightSplices (boolean setFlag)
void	setMinNumberOfSplices (int minSpliceSupport)
void	setExtensionFactor (int extensionFactor)
void	setMaskFileData (Map< String, Integer > maskedRegionMap)
void	setMinimumMappingQuality (double minMapQual)
void	setTrimQuantile (double quantile)
AlignmentDataModelStats	getData ()
double	getLambda (String chr) throws IOException
double	getSum (String chr) throws IOException
double	getNumberOfReads (String chr) throws IOException
double	getNumberMarkers (String chr) throws IOException
double	getNumberOfBPs ()
int	getCount (Collection< Annotation > Annotation) throws IOException
int[]	getGeneCounts (Collection< Gene > genes) throws IOException
int[]	getGeneCountsWithoutDatasetTotals (Collection< Gene > genes) throws IOException
double[]	getCountsPerBp (Annotation align, IntervalTree< Alignment > tree)
List< Double >	getCountsPerBp (Gene gene, IntervalTree< Alignment > tree)
Map< Gene, double[]>	getGeneExpression (Collection< Gene > genes) throws IOException
int	getCounts (Map< String, IntervalTree< Annotation >> geneTree, Collection< String > multimappers) throws IOException
int	getChromosomeLength (String chr)
Map< String, Integer >	getChromosomeLengths ()
double[]	getDataForAlignment (Annotation align) throws IOException
List< Double >	getDataForGene (Gene gene) throws IOException
Map< Gene, List< Double > >	getDataForGene (Collection< Gene > Annotation) throws IOException
AlignmentDataModelStats	getPairedData ()
Collection< Annotation >	scan (int[] windowSizes, double alpha) throws IOException
Collection< Annotation >	scan (int[] windowSizes, double alpha, String chr) throws IOException
void	scanGenome (ContinuousDataAlignmentModel data2, int windowSize, String chr, FileWriter writer, boolean filterSignificance) throws IOException
double[]	scanPRate (Gene gene) throws IOException
double[]	scanPRate (Gene gene, IntervalTree< Alignment > tree) throws IOException
double[]	scanPRate (Gene gene, IntervalTree< Alignment > tree, double localLambda) throws IOException
double[]	scanPRate (Gene gene, IntervalTree< Alignment > tree, double localLambda, int numMarkers) throws IOException
double[]	scanRegion (int fixedWidth, LightweightGenomicAnnotation region) throws IOException
double[]	scoreSegment (Annotation align) throws IOException
Map< Annotation, double[]>	scoreSegments (Collection< Annotation > set) throws IOException
Map< Annotation, double[]>	scoreSegments (Collection< Annotation > set, String chrToUse) throws IOException
Map< Annotation, double[]>	scoreSegments (Collection< Annotation > set, String chrToUse, boolean ignoreAlpha) throws IOException
double[]	scoreGene (Gene align) throws IOException
double[]	scoreGene (Gene align, double localLambda) throws IOException
GeneScore	scoreGene (Gene align, IntervalTree< Alignment > tree, double localLambda) throws IOException
GeneScore	scoreGene (Gene align, IntervalTree< Alignment > tree, double localLambda, int numMarkers) throws IOException
Map< Gene, double[]>	scoreGenes (Collection< Gene > set, String chrToUse, IntervalTree< Alignment > tree) throws IOException
GeneScore	getPeak (Gene gene, Gene startCodon, IntervalTree< Alignment > tree) throws IOException
Gene	getPeak (Gene gene, Gene startCodon) throws IOException
AlignmentDataModelStats	getAlignmentDataModelStats ()
double[]	scoreGene (Gene align, IntervalTree< Alignment > tree) throws IOException
Map< Gene, double[]>	scoreGenes (Collection< Gene > genes) throws IOException
Map< Gene, double[]>	scoreGenes (Collection< Gene > set, String chrToUse) throws IOException
Map< Gene, double[]>	scoreGenes (Collection< Gene > set, String chrToUse, int size) throws IOException
void	scoreGenes (BEDFileParser genes) throws IOException
Map< Path, double[]>	scorePathsForOnlyRPKM (Collection< Path > paths)
Map< Path, double[]>	scorePaths (Collection< Path > paths, double lambda) throws IOException
double	count (Annotation align) throws IOException
Gene	trimMaxContiguous (Gene region, double quantile) throws IOException
List< Gene >	filterGenesByExpression (Map< Gene, List< Double >> countsMap)
Gene	trimGeneEnds (Gene gene, double quantile) throws IOException
void	writeConnections (String save, ChromosomeWithBubblesJGraphT graph) throws IOException
boolean	hasDataForChromosome (String chr)
void	resetTreeCache ()
double	CV (Gene gene, IntervalTree< Alignment > tree) throws IOException
Collection< Annotation >	permuteRegions (Annotation align) throws IOException
Collection< Annotation >	rawRegions (Annotation align) throws IOException
int	getBasesCovered (Annotation region) throws IOException
int	getBasesCovered (Annotation region, int EF) throws IOException

Static Public Member Functions
static int[]	getWidths (String str)
static Map< Path, double[]>	scorePaths (Collection< Path > paths, ChromosomeWithBubblesJGraphT graph, double alpha)
static Map< Path, double[]>	scorePaths (Collection< Path > paths, double lambda, double numMarkers, double numReads, double RPKMContant, Map< Annotation, Double > localRates, double alpha)
static double	calculatePVal (int k, double lambda, double w, double T)
static void	writeFullBED (String save, Map< Gene, double[]> map, double alpha) throws IOException
static void	writeFullBED (String save, Collection< Gene > segments) throws IOException
static void	main (String[] args) throws Exception
static Collection< Gene >	filterPaths (Map< Path, double[]> scores, double alpha2)
static Map< String, Integer >	parseMaskFiles (File[] files) throws IOException

Static Public Attributes
static int	DEFAULT_MIN_MAPPING_QUALITY = 5
static int	DEFAULT_INSERT_SIZE_FUDGE = 20
static double	DEFAULT_INS_SIZE_PVAL = 0.05
static double	DEFAULT_MAKE_GENE_OVERLAP = 0.3

Constructor & Destructor Documentation

broad.pda.seq.segmentation.ContinuousDataAlignmentModel.ContinuousDataAlignmentModel

(

AlignmentDataModel

data

)

throws IOException

Constructor to build the data alignment model

Parameters

data	the alignment data model that stores the read data

Exceptions

IOException

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broad.pda.seq.segmentation.ContinuousDataAlignmentModel.ContinuousDataAlignmentModel

(

AlignmentDataModelStats

data

)

throws IOException

Constructor to build the data alignment model

Parameters

data	the alignment data model that computes the statistics and stores the read data

Exceptions

IOException

broad.pda.seq.segmentation.ContinuousDataAlignmentModel.ContinuousDataAlignmentModel	(	AlignmentDataModelStats	data,
		int	EF,
		int	minSpliceSupport
	)		throws IOException

Constructor to build the data alignment model

Parameters

data	the alignment data model that computes the statistics and stores the read data
EF	an extension factor used to extend reads
minSpliceSupport	the minimum number of spliced reads needed to add a connection in the graph

Exceptions

IOException

broad.pda.seq.segmentation.ContinuousDataAlignmentModel.ContinuousDataAlignmentModel	(	AlignmentDataModelStats	data,
		File[]	maskFiles,
		int	minSpliceSupport
	)		throws IOException

Constructor to build the data alignment model

Parameters

data	the alignment data model that computes the statistics and stores the read data
maskFiles	the mask files
minSpliceSupport	the minimum number of spliced reads needed to add a connection in the graph

Exceptions

IOException

broad.pda.seq.segmentation.ContinuousDataAlignmentModel.ContinuousDataAlignmentModel	(	AlignmentDataModelStats	data,
		File[]	maskFiles,
		int	EF,
		int	minSpliceSupport,
		AlignmentDataModelStats	pairedData,
		AlignmentDataModelStats	strandSpecificReads
	)		throws IOException

Constructor to build the data alignment model

Parameters

data	the alignment data model that computes the statistics and stores the read data
maskFiles	the mask files
EF	an extension factor used to extend reads
minSpliceSupport	the minimum number of spliced reads needed to add a connection in the graph
pairedData	the alignment data model that stores the stats for paired end reads and the paired end read data
strandSpecificReads	an alignment data model for the strand specific reads

Exceptions

IOException

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broad.pda.seq.segmentation.ContinuousDataAlignmentModel.ContinuousDataAlignmentModel	(	AlignmentDataModelStats	data,
		File[]	maskFiles,
		int	EF,
		int	minSpliceSupport,
		AlignmentDataModelStats	pairedData,
		AlignmentDataModelStats	strandSpecificReads,
		boolean	upweight
	)		throws IOException

Constructor to build the data alignment model

Parameters

data	the alignment data model that computes the statistics and stores the read data
maskFiles	the mask files
EF	an extension factor used to extend reads
minSpliceSupport	the minimum number of spliced reads needed to add a connection in the graph
pairedData	the alignment data model that stores the stats for paired end reads and the paired end read data
strandSpecificReads	an alignment data model for the strand specific reads
chunkSize	the size of the cache chunk used

Exceptions

IOException

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broad.pda.seq.segmentation.ContinuousDataAlignmentModel.ContinuousDataAlignmentModel	(	AlignmentDataModelStats	data,
		Map< String, Integer >	maskFileData,
		int	EF,
		int	minSpliceSupport,
		AlignmentDataModelStats	pairedData,
		AlignmentDataModelStats	strandSpecificReads
	)		throws IOException

Constructor to build the data alignment model

Parameters

data	the alignment data model that computes the statistics and stores the read data
maskFileData	a map of all unalignable regions of the genome
EF	an extension factor used to extend reads
minSpliceSupport	the minimum number of spliced reads needed to add a connection in the graph
pairedData	the alignment data model that stores the stats for paired end reads and the paired end read data
strandSpecificReads	an alignment data model for the strand specific reads

Exceptions

IOException

broad.pda.seq.segmentation.ContinuousDataAlignmentModel.ContinuousDataAlignmentModel	(	AlignmentDataModelStats	data,
		Map< String, Integer >	maskFileData,
		int	EF,
		int	minSpliceSupport,
		AlignmentDataModelStats	pairedData,
		AlignmentDataModelStats	strandSpecificReads,
		boolean	upWeight
	)		throws IOException

Constructor to build the data alignment model

Parameters

data	the alignment data model that computes the statistics and stores the read data
maskFileData	a map of all unalignable regions of the genome
EF	an extension factor used to extend reads
minSpliceSupport	the minimum number of spliced reads needed to add a connection in the graph
pairedData	the alignment data model that stores the stats for paired end reads and the paired end read data
strandSpecificReads	an alignment data model for the strand specific reads
upWeightSplices	whether to weight spliced reads based on their proportioncoverage scores

Exceptions

IOException

broad.pda.seq.segmentation.ContinuousDataAlignmentModel.ContinuousDataAlignmentModel	(	AlignmentDataModelStats	data,
		Map< String, Integer >	maskFileData,
		int	EF,
		int	minSpliceSupport,
		AlignmentDataModelStats	pairedData,
		AlignmentDataModelStats	strandSpecificReads,
		int	chunkSize,
		boolean	upWeightSplices
	)		throws IOException

Constructor to build the data alignment model

Parameters

data	the alignment data model that computes the statistics and stores the read data
maskFileData	a map of all unalignable regions of the genome
EF	an extension factor used to extend reads
minSpliceSupport	the minimum number of spliced reads needed to add a connection in the graph
pairedData	the alignment data model that stores the stats for paired end reads and the paired end read data
strandSpecificReads	an alignment data model for the strand specific reads
chunkSize	the size of the cache chunk used
upWeightSplices	whether to weight spliced reads based on their proportion when computing coverage scores

Exceptions

IOException

broad.pda.seq.segmentation.ContinuousDataAlignmentModel.ContinuousDataAlignmentModel	(	AlignmentDataModelStats	data,
		File[]	maskFiles,
		int	EF,
		int	minSpliceSupport,
		AlignmentDataModelStats	pairedData
	)		throws IOException

Constructor to build the data alignment model

Parameters

data	the alignment data model that computes the statistics and stores the read data
maskFiles	the mask files
EF	an extension factor used to extend reads
minSpliceSupport	the minimum number of spliced reads needed to add a connection in the graph
pairedData	the alignment data model that stores the stats for paired end reads and the paired end read data

Exceptions

IOException

broad.pda.seq.segmentation.ContinuousDataAlignmentModel.ContinuousDataAlignmentModel	(	AlignmentDataModelStats	data,
		File[]	maskFiles,
		int	EF,
		int	minSpliceSupport
	)		throws IOException

Constructor to build the data alignment model

Parameters

data	the alignment data model that computes the statistics and stores the read data
maskFiles	the mask files
EF	an extension factor used to extend reads
minSpliceSupport	the minimum number of spliced reads needed to add a connection in the graph

Exceptions

IOException

Member Function Documentation

static double broad.pda.seq.segmentation.ContinuousDataAlignmentModel.calculatePVal ( int  k, double  lambda, double  w, double  T  )

static

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double broad.pda.seq.segmentation.ContinuousDataAlignmentModel.count

(

Annotation

align

)

throws IOException

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double broad.pda.seq.segmentation.ContinuousDataAlignmentModel.CV	(	Gene	gene,
		IntervalTree< Alignment >	tree
	)		throws IOException

List<Gene> broad.pda.seq.segmentation.ContinuousDataAlignmentModel.filterGenesByExpression

(

Map< Gene, List< Double >>

countsMap

)

This function will filter the genes in the input Map by a number of constraints on the total number of reads on the genes

1. All genes with expression < 5.0 read counts will be removed
2. All genes with expression in the 75th quantile of the remaining expressed genes will be returned

   Parameters

   countsMap

   A map of RefSeqGene to a List of counts along the length of the gene

   Returns

static Collection<Gene> broad.pda.seq.segmentation.ContinuousDataAlignmentModel.filterPaths ( Map< Path, double[]>  scores, double  alpha2  )

static

AlignmentDataModelStats broad.pda.seq.segmentation.ContinuousDataAlignmentModel.getAlignmentDataModelStats

(

)

int broad.pda.seq.segmentation.ContinuousDataAlignmentModel.getBasesCovered

(

Annotation

region

)

throws IOException

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int broad.pda.seq.segmentation.ContinuousDataAlignmentModel.getBasesCovered	(	Annotation	region,
		int	EF
	)		throws IOException

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int broad.pda.seq.segmentation.ContinuousDataAlignmentModel.getChromosomeLength

(

String

chr

)

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

(

)

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int broad.pda.seq.segmentation.ContinuousDataAlignmentModel.getCount

(

Collection< Annotation >

Annotation

)

throws IOException

int broad.pda.seq.segmentation.ContinuousDataAlignmentModel.getCounts	(	Map< String, IntervalTree< Annotation >>	geneTree,
		Collection< String >	multimappers
	)		throws IOException

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double [] broad.pda.seq.segmentation.ContinuousDataAlignmentModel.getCountsPerBp	(	Annotation	align,
		IntervalTree< Alignment >	tree
	)

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List<Double> broad.pda.seq.segmentation.ContinuousDataAlignmentModel.getCountsPerBp	(	Gene	gene,
		IntervalTree< Alignment >	tree
	)

AlignmentDataModelStats broad.pda.seq.segmentation.ContinuousDataAlignmentModel.getData

(

)

Get the underlying AlignmentDataModelStats object

Returns

the AlignmentDataModelStats object

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double [] broad.pda.seq.segmentation.ContinuousDataAlignmentModel.getDataForAlignment

(

Annotation

align

)

throws IOException

This function returns an array of type double with counts for each base pair across the genomic region of the gene

Author

skadri

Parameters

align

Returns

Exceptions

IOException

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List<Double> broad.pda.seq.segmentation.ContinuousDataAlignmentModel.getDataForGene

(

Gene

gene

)

throws IOException

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Map<Gene, List<Double> > broad.pda.seq.segmentation.ContinuousDataAlignmentModel.getDataForGene

(

Collection< Gene >

Annotation

)

throws IOException

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int [] broad.pda.seq.segmentation.ContinuousDataAlignmentModel.getGeneCounts

(

Collection< Gene >

genes

)

throws IOException

int [] broad.pda.seq.segmentation.ContinuousDataAlignmentModel.getGeneCountsWithoutDatasetTotals

(

Collection< Gene >

genes

)

throws IOException

Map<Gene, double[]> broad.pda.seq.segmentation.ContinuousDataAlignmentModel.getGeneExpression

(

Collection< Gene >

genes

)

throws IOException

double broad.pda.seq.segmentation.ContinuousDataAlignmentModel.getLambda

(

String

chr

)

throws IOException

Get an estimate of the expected read coverage per base

Parameters

chr	chromosome to retrieve

Returns

lambda

Exceptions

IOException

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double broad.pda.seq.segmentation.ContinuousDataAlignmentModel.getNumberMarkers

(

String

chr

)

throws IOException

Gets the number of allowable bases per chr

Parameters

chr	chromosome to retrieve

Returns

total number of allowable bases

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double broad.pda.seq.segmentation.ContinuousDataAlignmentModel.getNumberOfBPs

(

)

Get total number of bases

Returns

total number of bases

double broad.pda.seq.segmentation.ContinuousDataAlignmentModel.getNumberOfReads

(

String

chr

)

throws IOException

Gets the total number of reads per chr

Parameters

chr	chromosome to retrieve

Returns

total number of reads

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AlignmentDataModelStats broad.pda.seq.segmentation.ContinuousDataAlignmentModel.getPairedData

(

)

GeneScore broad.pda.seq.segmentation.ContinuousDataAlignmentModel.getPeak	(	Gene	gene,
		Gene	startCodon,
		IntervalTree< Alignment >	tree
	)		throws IOException

Gene broad.pda.seq.segmentation.ContinuousDataAlignmentModel.getPeak	(	Gene	gene,
		Gene	startCodon
	)		throws IOException

double broad.pda.seq.segmentation.ContinuousDataAlignmentModel.getSum

(

String

chr

)

throws IOException

Gets the total number of reads per chr

Parameters

chr	chromosome to retrieve

Returns

total number of reads

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static int [] broad.pda.seq.segmentation.ContinuousDataAlignmentModel.getWidths ( String  str )

static

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boolean broad.pda.seq.segmentation.ContinuousDataAlignmentModel.hasDataForChromosome

(

String

chr

)

static void broad.pda.seq.segmentation.ContinuousDataAlignmentModel.main ( String[]  args ) throws Exception

static

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static Map<String, Integer> broad.pda.seq.segmentation.ContinuousDataAlignmentModel.parseMaskFiles ( File[]  files ) throws IOException

static

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Collection<Annotation> broad.pda.seq.segmentation.ContinuousDataAlignmentModel.permuteRegions

(

Annotation

align

)

throws IOException

Collection<Annotation> broad.pda.seq.segmentation.ContinuousDataAlignmentModel.rawRegions

(

Annotation

align

)

throws IOException

void broad.pda.seq.segmentation.ContinuousDataAlignmentModel.resetTreeCache

(

)

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Collection<Annotation> broad.pda.seq.segmentation.ContinuousDataAlignmentModel.scan	(	int[]	windowSizes,
		double	alpha
	)		throws IOException

Collection<Annotation> broad.pda.seq.segmentation.ContinuousDataAlignmentModel.scan	(	int[]	windowSizes,
		double	alpha,
		String	chr
	)		throws IOException

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void broad.pda.seq.segmentation.ContinuousDataAlignmentModel.scanGenome	(	ContinuousDataAlignmentModel	data2,
		int	windowSize,
		String	chr,
		FileWriter	writer,
		boolean	filterSignificance
	)		throws IOException

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double [] broad.pda.seq.segmentation.ContinuousDataAlignmentModel.scanPRate

(

Gene

gene

)

throws IOException

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

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

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

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

double [] broad.pda.seq.segmentation.ContinuousDataAlignmentModel.scoreGene

(

Gene

align

)

throws IOException

Parameters

align

Returns

{calculatePVal(new Double(sum).intValue(), localLambda, geneLength, getNumberMarkers(chr)), enrich, sum, avgCoverage, rpkm, localLambda, geneLength,nominalP, fullyContained}

Exceptions

IOException

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double [] broad.pda.seq.segmentation.ContinuousDataAlignmentModel.scoreGene	(	Gene	align,
		double	localLambda
	)		throws IOException

GeneScore broad.pda.seq.segmentation.ContinuousDataAlignmentModel.scoreGene	(	Gene	align,
		IntervalTree< Alignment >	tree,
		double	localLambda
	)		throws IOException

GeneScore broad.pda.seq.segmentation.ContinuousDataAlignmentModel.scoreGene	(	Gene	align,
		IntervalTree< Alignment >	tree,
		double	localLambda,
		int	numMarkers
	)		throws IOException

double [] broad.pda.seq.segmentation.ContinuousDataAlignmentModel.scoreGene	(	Gene	align,
		IntervalTree< Alignment >	tree
	)		throws IOException

Map<Gene, double[]> broad.pda.seq.segmentation.ContinuousDataAlignmentModel.scoreGenes	(	Collection< Gene >	set,
		String	chrToUse,
		IntervalTree< Alignment >	tree
	)		throws IOException

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Map<Gene, double[]> broad.pda.seq.segmentation.ContinuousDataAlignmentModel.scoreGenes

(

Collection< Gene >

genes

)

throws IOException

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Map<Gene, double[]> broad.pda.seq.segmentation.ContinuousDataAlignmentModel.scoreGenes	(	Collection< Gene >	set,
		String	chrToUse
	)		throws IOException

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Map<Gene, double[]> broad.pda.seq.segmentation.ContinuousDataAlignmentModel.scoreGenes	(	Collection< Gene >	set,
		String	chrToUse,
		int	size
	)		throws IOException

void broad.pda.seq.segmentation.ContinuousDataAlignmentModel.scoreGenes

(

BEDFileParser

genes

)

throws IOException

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Map<Path, double[]> broad.pda.seq.segmentation.ContinuousDataAlignmentModel.scorePaths	(	Collection< Path >	paths,
		double	lambda
	)		throws IOException

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static Map<Path, double[]> broad.pda.seq.segmentation.ContinuousDataAlignmentModel.scorePaths ( Collection< Path >  paths, ChromosomeWithBubblesJGraphT  graph, double  alpha  )

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static Map<Path, double[]> broad.pda.seq.segmentation.ContinuousDataAlignmentModel.scorePaths ( Collection< Path >  paths, double  lambda, double  numMarkers, double  numReads, double  RPKMContant, Map< Annotation, Double >  localRates, double  alpha  )

static

Map<Path, double[]> broad.pda.seq.segmentation.ContinuousDataAlignmentModel.scorePathsForOnlyRPKM

(

Collection< Path >

paths

)

double [] broad.pda.seq.segmentation.ContinuousDataAlignmentModel.scoreSegment

(

Annotation

align

)

throws IOException

Map<Annotation, double[]> broad.pda.seq.segmentation.ContinuousDataAlignmentModel.scoreSegments

(

Collection< Annotation >

set

)

throws IOException

Map<Annotation, double[]> broad.pda.seq.segmentation.ContinuousDataAlignmentModel.scoreSegments	(	Collection< Annotation >	set,
		String	chrToUse
	)		throws IOException

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Map<Annotation, double[]> broad.pda.seq.segmentation.ContinuousDataAlignmentModel.scoreSegments	(	Collection< Annotation >	set,
		String	chrToUse,
		boolean	ignoreAlpha
	)		throws IOException

void broad.pda.seq.segmentation.ContinuousDataAlignmentModel.setAlpha

(

double

alpha

)

void broad.pda.seq.segmentation.ContinuousDataAlignmentModel.setExtensionFactor

(

int

extensionFactor

)

void broad.pda.seq.segmentation.ContinuousDataAlignmentModel.setFindMaxContiguous

(

boolean

findMaxContiguous

)

void broad.pda.seq.segmentation.ContinuousDataAlignmentModel.setMaskFileData

(

Map< String, Integer >

maskedRegionMap

)

void broad.pda.seq.segmentation.ContinuousDataAlignmentModel.setMinContguousSegmentSize

(

int

minSize

)

void broad.pda.seq.segmentation.ContinuousDataAlignmentModel.setMinimumMappingQuality

(

double

minMapQual

)

void broad.pda.seq.segmentation.ContinuousDataAlignmentModel.setMinNumberOfSplices

(

int

minSpliceSupport

)

void broad.pda.seq.segmentation.ContinuousDataAlignmentModel.setTrimEnds

(

boolean

trimEnds

)

void broad.pda.seq.segmentation.ContinuousDataAlignmentModel.setTrimQuantile

(

double

quantile

)

void broad.pda.seq.segmentation.ContinuousDataAlignmentModel.setUpWeightSplices

(

boolean

setFlag

)

Gene broad.pda.seq.segmentation.ContinuousDataAlignmentModel.trimGeneEnds	(	Gene	gene,
		double	quantile
	)		throws IOException

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Gene broad.pda.seq.segmentation.ContinuousDataAlignmentModel.trimMaxContiguous	(	Gene	region,
		double	quantile
	)		throws IOException

Trim a region to a contiguous subregion with max number of positions having coverage above the quantile

Parameters

region	The original region
quantile	The coverage quantile of the original region

Returns

The contiguous subregion with maximal number of positions having coverage above the quantile of the original region or null if can't trim

Exceptions

IOException

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void broad.pda.seq.segmentation.ContinuousDataAlignmentModel.writeConnections	(	String	save,
		ChromosomeWithBubblesJGraphT	graph
	)		throws IOException

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static void broad.pda.seq.segmentation.ContinuousDataAlignmentModel.writeFullBED ( String  save, Map< Gene, double[]>  map, double  alpha  ) throws IOException

static

static void broad.pda.seq.segmentation.ContinuousDataAlignmentModel.writeFullBED ( String  save, Collection< Gene >  segments  ) throws IOException

static

Member Data Documentation

double broad.pda.seq.segmentation.ContinuousDataAlignmentModel.DEFAULT_INS_SIZE_PVAL = 0.05

static

int broad.pda.seq.segmentation.ContinuousDataAlignmentModel.DEFAULT_INSERT_SIZE_FUDGE = 20

static

double broad.pda.seq.segmentation.ContinuousDataAlignmentModel.DEFAULT_MAKE_GENE_OVERLAP = 0.3

static

int broad.pda.seq.segmentation.ContinuousDataAlignmentModel.DEFAULT_MIN_MAPPING_QUALITY = 5

static

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

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