broad.pda.seq.clip.GenomeSpaceSampleData Member List

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

data	broad.pda.seq.clip.SampleData	protected
expressionByScanPval	broad.pda.seq.clip.SampleData	protected
expressionCutoffValue	broad.pda.seq.clip.SampleData	protected
firstReadTranscriptionStrand()	broad.pda.seq.clip.SampleData
fullyContainedReads	broad.pda.seq.clip.SampleData	protected
geneAvgCoverage	broad.pda.seq.clip.SampleData	protected
genesByChr	broad.pda.seq.clip.SampleData	protected
genesByName	broad.pda.seq.clip.SampleData	protected
geneScores	broad.pda.seq.clip.SampleData	protected
GenomeSpaceSampleData(String bamFile, String chrSizeFile, Map< String, Collection< Gene >> genes, double expressionCutoff, boolean fullyContained)	broad.pda.seq.clip.GenomeSpaceSampleData
getData()	broad.pda.seq.clip.SampleData
getEnrichmentOverGene(Gene gene, Annotation window)	broad.pda.seq.clip.SampleData
getExpressionScanPvalueCutoff()	broad.pda.seq.clip.SampleData
getFragmentLengthFilterData()	broad.pda.seq.clip.SampleData
getFragmentLengthGeneCount(Gene gene)	broad.pda.seq.clip.SampleData
getGeneAverageCoverage(Gene gene)	broad.pda.seq.clip.SampleData
getGeneCount(Gene gene)	broad.pda.seq.clip.SampleData
getGenePval(Gene gene)	broad.pda.seq.clip.GenomeSpaceSampleData
getGeneScanPval(Gene gene)	broad.pda.seq.clip.SampleData
getLogger()	broad.pda.seq.clip.SampleData
getOriginalBamFile()	broad.pda.seq.clip.SampleData
getSampleName()	broad.pda.seq.clip.SampleData
hashCode()	broad.pda.seq.clip.SampleData
isExpressed(Gene gene)	broad.pda.seq.clip.GenomeSpaceSampleData
logger	broad.pda.seq.clip.SampleData	static
maxFragmentLengthData	broad.pda.seq.clip.SampleData	protected
maxFragmentLengthGeneScores	broad.pda.seq.clip.SampleData	protected
SampleData(String bamFile, boolean firstReadTranscriptionStrand, Map< String, Collection< Gene >> genes, double expressionCutoff, boolean expByScanPval, boolean fullyContained)	broad.pda.seq.clip.SampleData
sampleName	broad.pda.seq.clip.SampleData	protected
setExpressionScanPvalueCutoff(double expressionScanPvalCutoff)	broad.pda.seq.clip.SampleData
setSampleName(String name)	broad.pda.seq.clip.SampleData