broad.pda.seq.protection.GenomeSpaceSampleData Member List

This is the complete list of members for broad.pda.seq.protection.GenomeSpaceSampleData, including all inherited members.

data	broad.pda.seq.protection.SampleData	protected
expressionByScanPval	broad.pda.seq.protection.SampleData	protected
expressionCutoffValue	broad.pda.seq.protection.SampleData	protected
firstReadTranscriptionStrand()	broad.pda.seq.protection.SampleData
fullyContainedReads	broad.pda.seq.protection.SampleData	protected
geneAvgCoverage	broad.pda.seq.protection.SampleData	protected
genesByChr	broad.pda.seq.protection.SampleData	protected
genesByName	broad.pda.seq.protection.SampleData	protected
geneScores	broad.pda.seq.protection.SampleData	protected
GenomeSpaceSampleData(String bamFile, String chrSizeFile, Map< String, Collection< Gene >> genes, int window, int step, double expressionCutoff, boolean fullyContained)	broad.pda.seq.protection.GenomeSpaceSampleData
getData()	broad.pda.seq.protection.SampleData
getEnrichmentOverGene(Gene gene, Annotation window)	broad.pda.seq.protection.SampleData
getExpressionScanPvalueCutoff()	broad.pda.seq.protection.SampleData
getFragmentLengthFilterData()	broad.pda.seq.protection.SampleData
getGeneAverageCoverage(Gene gene)	broad.pda.seq.protection.SampleData
getGeneCount(Gene gene)	broad.pda.seq.protection.SampleData
getGeneScanPval(Gene gene)	broad.pda.seq.protection.GenomeSpaceSampleData
getLogger()	broad.pda.seq.protection.SampleData
getOriginalBamFile()	broad.pda.seq.protection.SampleData
getSampleName()	broad.pda.seq.protection.SampleData
getStepSize()	broad.pda.seq.protection.SampleData
getWindowCount(Gene gene, Annotation window)	broad.pda.seq.protection.SampleData
getWindowScores(Gene gene)	broad.pda.seq.protection.SampleData
getWindowSize()	broad.pda.seq.protection.SampleData
gotWindowScoresFromFile()	broad.pda.seq.protection.SampleData
hashCode()	broad.pda.seq.protection.SampleData
isExpressed(Gene gene)	broad.pda.seq.protection.GenomeSpaceSampleData
logger	broad.pda.seq.protection.SampleData	protectedstatic
maxFragmentLengthData	broad.pda.seq.protection.SampleData	protected
SampleData(String bamFile, boolean firstReadTranscriptionStrand, Map< String, Collection< Gene >> genes, int window, int step, double expressionCutoff, boolean expByScanPval, boolean fullyContained)	broad.pda.seq.protection.SampleData
sampleName	broad.pda.seq.protection.SampleData	protected
scoreWindow(Gene gene, Annotation window)	broad.pda.seq.protection.SampleData
scoreWindow(Gene gene, Annotation window, double count)	broad.pda.seq.protection.SampleData
scoreWindowWithFragmentLengthFilter(Gene gene, Annotation window)	broad.pda.seq.protection.SampleData
setExpressionScanPvalueCutoff(double expressionScanPvalCutoff)	broad.pda.seq.protection.SampleData
setSampleName(String name)	broad.pda.seq.protection.SampleData
stepSize	broad.pda.seq.protection.SampleData	protected
trimMaxContiguous(Annotation window, List< Double > data, double quantile)	broad.pda.seq.protection.SampleData	static
windowScores	broad.pda.seq.protection.SampleData	protected
windowSize	broad.pda.seq.protection.SampleData	protected