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

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

Public Member Functions
	GenomeSpaceSampleData (String bamFile, String chrSizeFile, Map< String, Collection< Gene >> genes, double expressionCutoff, boolean fullyContained) throws IOException

boolean	isExpressed (Gene gene)

double	getGenePval (Gene gene)

Public Member Functions inherited from broad.pda.seq.clip.SampleData
	SampleData (String bamFile, boolean firstReadTranscriptionStrand, Map< String, Collection< Gene >> genes, double expressionCutoff, boolean expByScanPval, boolean fullyContained) throws IOException

int	hashCode ()

void	setExpressionScanPvalueCutoff (double expressionScanPvalCutoff)

double	getExpressionScanPvalueCutoff ()

double	getGeneCount (Gene gene)

double	getFragmentLengthGeneCount (Gene gene)

double	getGeneScanPval (Gene gene)

double	getGeneAverageCoverage (Gene gene)

boolean	isExpressed (Gene gene)

boolean	firstReadTranscriptionStrand ()

double	getEnrichmentOverGene (Gene gene, Annotation window)

Logger	getLogger ()

String	getSampleName ()

String	getOriginalBamFile ()

void	setSampleName (String name)

TranscriptomeSpaceAlignmentModel	getData ()

TranscriptomeSpaceAlignmentModel	getFragmentLengthFilterData ()

Additional Inherited Members
Static Public Attributes inherited from broad.pda.seq.clip.SampleData
static Logger	logger = Logger.getLogger(SampleData.class.getName())

Protected Attributes inherited from broad.pda.seq.clip.SampleData
String	sampleName

TranscriptomeSpaceAlignmentModel	data

TranscriptomeSpaceAlignmentModel	maxFragmentLengthData

Map< Gene, ScanStatisticScore >	maxFragmentLengthGeneScores

Map< Gene, ScanStatisticScore >	geneScores

Map< Gene, Double >	geneAvgCoverage

Map< String, Collection< Gene > >	genesByChr

Map< String, Gene >	genesByName

double	expressionCutoffValue

boolean	expressionByScanPval

boolean	fullyContainedReads

Detailed Description

Constructor & Destructor Documentation

broad.pda.seq.clip.GenomeSpaceSampleData.GenomeSpaceSampleData	(	String	bamFile,
		String	chrSizeFile,
		Map< String, Collection< Gene >>	genes,
		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

double broad.pda.seq.clip.GenomeSpaceSampleData.getGenePval ( 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

boolean broad.pda.seq.clip.GenomeSpaceSampleData.isExpressed ( Gene gene )

Whether the gene is significantly expressed genome wide

Parameters

gene The gene

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