| allSamples | broad.pda.seq.protection.MultiSampleScanPeakCaller | protected |
| binomialWindowScores | broad.pda.seq.protection.MultiSampleScanPeakCaller | protected |
| closeFilterRejectWriters() | broad.pda.seq.protection.MultiSampleScanPeakCaller | protected |
| commandLineHasDebugFlag(String[] commandArgs) | broad.pda.seq.protection.MultiSampleScanPeakCaller | protectedstatic |
| commandLineOutDir(String[] commandArgs) | broad.pda.seq.protection.MultiSampleScanPeakCaller | protectedstatic |
| controlSamples | broad.pda.seq.protection.MultiSampleScanPeakCaller | protected |
| createFromCommandArgs(String[] commandArgs) | broad.pda.seq.protection.MultiSampleScanPeakCaller | protectedstatic |
| expressionData | broad.pda.seq.protection.MultiSampleScanPeakCaller | protected |
| FILTER_REJECT_DIR | broad.pda.seq.protection.MultiSampleScanPeakCaller | protectedstatic |
| genes | broad.pda.seq.protection.MultiSampleScanPeakCaller | protected |
| getCoordinateSpace() | broad.pda.seq.protection.MultiSampleScanPeakCaller | |
| getOneRandomSamplePermutation() | broad.pda.seq.protection.MultiSampleScanPeakCaller | protected |
| getPeakBedFileName(SampleData sample, String outDir, String chrName) | broad.pda.seq.protection.MultiSampleScanPeakCaller | protected |
| getSingleSampleScanPeaks(SampleData sample, Gene gene) | broad.pda.seq.protection.MultiSampleScanPeakCaller | |
| initializeFilterRejectWriters(String commonSuffix, String outDir) | broad.pda.seq.protection.MultiSampleScanPeakCaller | protected |
| isExpressed(Gene gene) | broad.pda.seq.protection.MultiSampleScanPeakCaller | |
| isExpressedInAllControlSamples(Gene gene) | broad.pda.seq.protection.MultiSampleScanPeakCaller | |
| logger | broad.pda.seq.protection.MultiSampleScanPeakCaller | protectedstatic |
| main(String[] args) | broad.pda.seq.protection.MultiSampleScanPeakCaller | static |
| mergePeaks(Collection< Annotation > peaks) | broad.pda.seq.protection.MultiSampleScanPeakCaller | |
| MultiSampleScanPeakCaller(MultiSampleScanPeakCaller other) | broad.pda.seq.protection.MultiSampleScanPeakCaller | protected |
| MultiSampleScanPeakCaller(String sampleListFile, String bedFile, String chrSizeFile, int window, int step) | broad.pda.seq.protection.MultiSampleScanPeakCaller | |
| MultiSampleScanPeakCaller(String expressionBamFile, String signalBamFile, String bedFile, String chrSizeFile) | broad.pda.seq.protection.MultiSampleScanPeakCaller | |
| MultiSampleScanPeakCaller(String expressionBamFile, String signalBamFile, String bedFile, String chrSizeFile, int window, int step) | broad.pda.seq.protection.MultiSampleScanPeakCaller | |
| numControls | broad.pda.seq.protection.MultiSampleScanPeakCaller | protected |
| numSamples | broad.pda.seq.protection.MultiSampleScanPeakCaller | protected |
| numSignals | broad.pda.seq.protection.MultiSampleScanPeakCaller | protected |
| random | broad.pda.seq.protection.MultiSampleScanPeakCaller | protected |
| setBinomialScore(boolean binomialScore) | broad.pda.seq.protection.MultiSampleScanPeakCaller | |
| setCoordinateSpace(CoordinateSpace space) | broad.pda.seq.protection.MultiSampleScanPeakCaller | |
| setExpressionScanPvalueCutoff(double expressionScanPvalCutoff) | broad.pda.seq.protection.MultiSampleScanPeakCaller | |
| setExtraFields(boolean useExtraFields) | broad.pda.seq.protection.MultiSampleScanPeakCaller | |
| setFilterByStrand(boolean useStrandFilter) | broad.pda.seq.protection.MultiSampleScanPeakCaller | |
| setFirstReadTranscriptionStrand(boolean firstReadIsTranscriptionStrand) | broad.pda.seq.protection.MultiSampleScanPeakCaller | |
| setLoggerLevel(Level level) | broad.pda.seq.protection.MultiSampleScanPeakCaller | protected |
| setPeakCutoffMostCommonReplicate(double maxPct) | broad.pda.seq.protection.MultiSampleScanPeakCaller | |
| setPeakTrimQuantile(double trimPeakQuantile) | broad.pda.seq.protection.MultiSampleScanPeakCaller | |
| setPeakWindowCountCutoff(double peakCountCutoff) | broad.pda.seq.protection.MultiSampleScanPeakCaller | |
| setPeakWindowScanPvalCutoff(double peakScanPvalCutoff) | broad.pda.seq.protection.MultiSampleScanPeakCaller | |
| signalSamples | broad.pda.seq.protection.MultiSampleScanPeakCaller | protected |
| sizeFile | broad.pda.seq.protection.MultiSampleScanPeakCaller | protected |
| stepSize | broad.pda.seq.protection.MultiSampleScanPeakCaller | protected |
| windowSize | broad.pda.seq.protection.MultiSampleScanPeakCaller | protected |
| writeSingleSampleScanPeaks(SampleData sample, String outFile, String chrName) | broad.pda.seq.protection.MultiSampleScanPeakCaller | protected |
1.8.7
