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broad.pda.seq.clip.SampleData Member List

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

databroad.pda.seq.clip.SampleDataprotected
expressionByScanPvalbroad.pda.seq.clip.SampleDataprotected
expressionCutoffValuebroad.pda.seq.clip.SampleDataprotected
firstReadTranscriptionStrand()broad.pda.seq.clip.SampleData
fullyContainedReadsbroad.pda.seq.clip.SampleDataprotected
geneAvgCoveragebroad.pda.seq.clip.SampleDataprotected
genesByChrbroad.pda.seq.clip.SampleDataprotected
genesByNamebroad.pda.seq.clip.SampleDataprotected
geneScoresbroad.pda.seq.clip.SampleDataprotected
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
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.SampleData
loggerbroad.pda.seq.clip.SampleDatastatic
maxFragmentLengthDatabroad.pda.seq.clip.SampleDataprotected
maxFragmentLengthGeneScoresbroad.pda.seq.clip.SampleDataprotected
SampleData(String bamFile, boolean firstReadTranscriptionStrand, Map< String, Collection< Gene >> genes, double expressionCutoff, boolean expByScanPval, boolean fullyContained)broad.pda.seq.clip.SampleData
sampleNamebroad.pda.seq.clip.SampleDataprotected
setExpressionScanPvalueCutoff(double expressionScanPvalCutoff)broad.pda.seq.clip.SampleData
setSampleName(String name)broad.pda.seq.clip.SampleData