broad.pda.seq.protection.BatchedMultiSampleScanPeakCaller Member List

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

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
extendSuperArgsForSampleAndChr(String[] commandArgs, String sampleName, String chrName)	broad.pda.seq.protection.BatchedMultiSampleScanPeakCaller	static
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.BatchedMultiSampleScanPeakCaller	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