broad.pda.seq.protection.GenomeSpaceSampleData Class Reference

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

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

Public Member Functions
	GenomeSpaceSampleData (String bamFile, String chrSizeFile, Map< String, Collection< Gene >> genes, int window, int step, double expressionCutoff, boolean fullyContained) throws IOException
boolean	isExpressed (Gene gene)
double	getGeneScanPval (Gene gene)
Public Member Functions inherited from 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
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 ()

Additional Inherited Members
Static Public Member Functions inherited from broad.pda.seq.protection.SampleData
static Annotation	trimMaxContiguous (Annotation window, List< Double > data, double quantile)
Protected Attributes inherited from broad.pda.seq.protection.SampleData
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 inherited from broad.pda.seq.protection.SampleData
static Logger	logger = Logger.getLogger(SampleData.class.getName())

Detailed Description

Author

prussell

Constructor & Destructor Documentation

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

Parameters

bamFile	Bam alignment file
chrSizeFile	Chromosome size file
genes	Genes by chromosome
window	Window size
step	Step size
expressionCutoff	Genome wide scan P value cutoff for expression
fullyContained	Count fully contained reads only

Exceptions

IOException

Member Function Documentation

double broad.pda.seq.protection.GenomeSpaceSampleData.getGeneScanPval

(

Gene

gene

)

Get genome 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

boolean broad.pda.seq.protection.GenomeSpaceSampleData.isExpressed

(

Gene

gene

)

Whether the gene is significantly expressed genome wide

Parameters

gene

The gene

Returns

Whether the gene is expressed at the given significance level

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

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