broad.pda.seq.protection.SampleData Class Reference

Inheritance diagram for broad.pda.seq.protection.SampleData:

Collaboration diagram for broad.pda.seq.protection.SampleData:

Public Member Functions
	SampleData (String bamFile, boolean firstReadTranscriptionStrand, Map< String, Collection< Gene >> genes, int window, int step, double expressionCutoff, boolean expByScanPval, boolean fullyContained) throws IOException
int	hashCode ()
void	setExpressionScanPvalueCutoff (double expressionScanPvalCutoff)
double	getExpressionScanPvalueCutoff ()
double	getGeneCount (Gene gene)
double	getGeneScanPval (Gene gene)
double	getGeneAverageCoverage (Gene gene)
boolean	isExpressed (Gene gene)
double	getWindowCount (Gene gene, Annotation window)
boolean	firstReadTranscriptionStrand ()
Map< Annotation, ScanStatisticScore >	getWindowScores (Gene gene)
boolean	gotWindowScoresFromFile ()
double	getEnrichmentOverGene (Gene gene, Annotation window)
ScanStatisticScore	scoreWindowWithFragmentLengthFilter (Gene gene, Annotation window)
ScanStatisticScore	scoreWindow (Gene gene, Annotation window)
ScanStatisticScore	scoreWindow (Gene gene, Annotation window, double count)
Logger	getLogger ()
String	getSampleName ()
String	getOriginalBamFile ()
void	setSampleName (String name)
int	getWindowSize ()
int	getStepSize ()
TranscriptomeSpaceAlignmentModel	getData ()
TranscriptomeSpaceAlignmentModel	getFragmentLengthFilterData ()

Static Public Member Functions
static Annotation	trimMaxContiguous (Annotation window, List< Double > data, double quantile)

Protected Attributes
String	sampleName
TranscriptomeSpaceAlignmentModel	data
TranscriptomeSpaceAlignmentModel	maxFragmentLengthData
Map< Gene, ScanStatisticScore >	geneScores
Map< Gene, Double >	geneAvgCoverage
Map< Gene, Map< Annotation, ScanStatisticScore > >	windowScores
int	windowSize
int	stepSize
Map< String, Collection< Gene > >	genesByChr
Map< String, Gene >	genesByName
double	expressionCutoffValue
boolean	expressionByScanPval
boolean	fullyContainedReads

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

Detailed Description

Author

prussell

Constructor & Destructor Documentation

broad.pda.seq.protection.SampleData.SampleData	(	String	bamFile,
		boolean	firstReadTranscriptionStrand,
		Map< String, Collection< Gene >>	genes,
		int	window,
		int	step,
		double	expressionCutoff,
		boolean	expByScanPval,
		boolean	fullyContained
	)		throws IOException

Parameters

bamFile	Bam file
firstReadTranscriptionStrand	Whether read 1 is in direction of transcription
genes	Genes by chromosome
window	Window size
step	Step size
expressionCutoff	P value cutoff for scan test of gene expression
expByScanPval	Expression is assessed by scan P value. If false, uses average read depth
fullyContained	Count fully contained reads only

Exceptions

IOException

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Member Function Documentation

boolean broad.pda.seq.protection.SampleData.firstReadTranscriptionStrand

(

)

Whether read 1 is in direction of transcription

Returns

True iff first read transcription strand is true

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TranscriptomeSpaceAlignmentModel broad.pda.seq.protection.SampleData.getData

(

)

Write the window scores to a file for future use

Parameters

m	Multi sample binding site caller that this belongs to

Exceptions

IOException

Get the alignment data

Returns

Alignment model

double broad.pda.seq.protection.SampleData.getEnrichmentOverGene	(	Gene	gene,
		Annotation	window
	)

Get enrichment of a window over a gene

Parameters

gene	The gene
window	Window contained in the gene

Returns

Enrichment of window over gene background

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double broad.pda.seq.protection.SampleData.getExpressionScanPvalueCutoff

(

)

Get genome wide scan P value cutoff for expression of transcript

Returns

P value cutoff for transcript expression against genomic background

TranscriptomeSpaceAlignmentModel broad.pda.seq.protection.SampleData.getFragmentLengthFilterData

(

)

Get the alignment data filtered by max fragment length

Returns

Alignment model

double broad.pda.seq.protection.SampleData.getGeneAverageCoverage

(

Gene

gene

)

Get average coverage of gene Get score from cache or calculate and cache score

Parameters

gene

The gene

Returns

The average coverage of the gene

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double broad.pda.seq.protection.SampleData.getGeneCount

(

Gene

gene

)

Get number of fragments mapping to gene Get score from cache or calculate and cache score

Parameters

gene

The gene

Returns

The number of fragments mapping to the gene

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double broad.pda.seq.protection.SampleData.getGeneScanPval

(

Gene

gene

)

Get coordinate space wide scan P value of number of fragments mapping to the gene Get score from cache or calculate and cache score

Parameters

gene

The gene

Returns

The scan P value of the number of fragments mapping to the gene with respect to teh coordinate space

Logger broad.pda.seq.protection.SampleData.getLogger

(

)

Get the logger

Returns

The logger

String broad.pda.seq.protection.SampleData.getOriginalBamFile

(

)

Get name of original bam file

Returns

Bam file name

String broad.pda.seq.protection.SampleData.getSampleName

(

)

Get the sample name

Returns

Sample name

int broad.pda.seq.protection.SampleData.getStepSize

(

)

double broad.pda.seq.protection.SampleData.getWindowCount	(	Gene	gene,
		Annotation	window
	)

Get number of fragments mapping to gene window Get score from cache or calculate and cache score

Parameters

gene	The gene
window	The window

Returns

The number of fragments mapping to the gene

Map<Annotation, ScanStatisticScore> broad.pda.seq.protection.SampleData.getWindowScores

(

Gene

gene

)

Get scores for each window in the gene

Parameters

gene

The gene

Returns

The scores by window

int broad.pda.seq.protection.SampleData.getWindowSize

(

)

boolean broad.pda.seq.protection.SampleData.gotWindowScoresFromFile

(

)

Whether the window scores were read from an existing file

Returns

Whether the window scores were read from an existing file

int broad.pda.seq.protection.SampleData.hashCode

(

)

boolean broad.pda.seq.protection.SampleData.isExpressed

(

Gene

gene

)

Whether the gene is significantly expressed in the sample

Parameters

gene

The gene

Returns

Whether the gene is expressed at the given significance level

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ScanStatisticScore broad.pda.seq.protection.SampleData.scoreWindow	(	Gene	gene,
		Annotation	window
	)

Get scan statistic score for a specified window

Parameters

gene	Parent gene
window	The window

Returns

Scan statistic score for window with global stats referring to parent transcript

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ScanStatisticScore broad.pda.seq.protection.SampleData.scoreWindow	(	Gene	gene,
		Annotation	window,
		double	count
	)

Get scan statistic score for a specified window

Parameters

gene	Parent gene
window	The window
count	The number to use as the region count in score

Returns

Scan statistic score for window with global stats referring to parent transcript

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ScanStatisticScore broad.pda.seq.protection.SampleData.scoreWindowWithFragmentLengthFilter	(	Gene	gene,
		Annotation	window
	)

Get scan statistic score for a window based on filtering fragments overlapping the window by size

Parameters

gene	The gene
window	The window

Returns

Scan statistic score for window with global stats referring to parent transcript

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void broad.pda.seq.protection.SampleData.setExpressionScanPvalueCutoff

(

double

expressionScanPvalCutoff

)

Set genome wide scan P value cutoff for expression of transcript

Parameters

expressionScanPvalCutoff

P value cutoff for transcript expression against genomic background

void broad.pda.seq.protection.SampleData.setSampleName

(

String

name

)

Set the sample name

Parameters

name	Sample name

static Annotation broad.pda.seq.protection.SampleData.trimMaxContiguous ( Annotation  window, List< Double >  data, double  quantile  )

static

Trim the region to max contiguous subregion above a certain quantile

Parameters

window	The region
data	Position level list of counts within the region
quantile	Quantile for trim max contiguous

Returns

Trimmed region

Member Data Documentation

TranscriptomeSpaceAlignmentModel broad.pda.seq.protection.SampleData.data

protected

boolean broad.pda.seq.protection.SampleData.expressionByScanPval

protected

double broad.pda.seq.protection.SampleData.expressionCutoffValue

protected

boolean broad.pda.seq.protection.SampleData.fullyContainedReads

protected

Map<Gene, Double> broad.pda.seq.protection.SampleData.geneAvgCoverage

protected

Map<String, Collection<Gene> > broad.pda.seq.protection.SampleData.genesByChr

protected

Map<String, Gene> broad.pda.seq.protection.SampleData.genesByName

protected

Map<Gene, ScanStatisticScore> broad.pda.seq.protection.SampleData.geneScores

protected

Logger broad.pda.seq.protection.SampleData.logger = Logger.getLogger(SampleData.class.getName())

staticprotected

TranscriptomeSpaceAlignmentModel broad.pda.seq.protection.SampleData.maxFragmentLengthData

protected

String broad.pda.seq.protection.SampleData.sampleName

protected

int broad.pda.seq.protection.SampleData.stepSize

protected

Map<Gene, Map<Annotation, ScanStatisticScore> > broad.pda.seq.protection.SampleData.windowScores

protected

int broad.pda.seq.protection.SampleData.windowSize

protected

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

• java/broad/pda/seq/protection/SampleData.java