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broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller Member List

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

backgroundDatabroad.pda.seq.protection.TwoSampleScanSkellamPeakCallerprotected
backgroundNamebroad.pda.seq.protection.TwoSampleScanSkellamPeakCallerprotected
backgroundProcessorbroad.pda.seq.protection.TwoSampleScanSkellamPeakCallerprotected
backgroundScanPvaluesbroad.pda.seq.protection.TwoSampleScanSkellamPeakCallerprotected
EXPRESSION_PVALUE_CUTOFFbroad.pda.seq.protection.TwoSampleScanSkellamPeakCallerstatic
filterWindows(Collection< Annotation > windows)broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller
genesbroad.pda.seq.protection.TwoSampleScanSkellamPeakCallerprotected
getPoissonLambda(int regionLength, double d, int windowSize)broad.pda.seq.protection.TwoSampleScanSkellamPeakCallerstatic
getSkellamPvalue(double backgroundLambda, double signalLambda, int backgroundCount, int signalCount)broad.pda.seq.protection.TwoSampleScanSkellamPeakCallerprotectedstatic
loggerbroad.pda.seq.protection.TwoSampleScanSkellamPeakCallerprotectedstatic
MIN_WINDOW_COUNTbroad.pda.seq.protection.TwoSampleScanSkellamPeakCallerprotectedstatic
pValueCutoffScanbroad.pda.seq.protection.TwoSampleScanSkellamPeakCallerprotected
pValueCutoffSkellambroad.pda.seq.protection.TwoSampleScanSkellamPeakCallerprotected
signalDatabroad.pda.seq.protection.TwoSampleScanSkellamPeakCallerprotected
signalNamebroad.pda.seq.protection.TwoSampleScanSkellamPeakCallerprotected
signalProcessorbroad.pda.seq.protection.TwoSampleScanSkellamPeakCallerprotected
stepSizebroad.pda.seq.protection.TwoSampleScanSkellamPeakCallerprotected
transcriptomeSpacebroad.pda.seq.protection.TwoSampleScanSkellamPeakCallerprotected
trimPeak(Gene window)broad.pda.seq.protection.TwoSampleScanSkellamPeakCallerprotected
trimPeakByQuantilebroad.pda.seq.protection.TwoSampleScanSkellamPeakCallerprotected
windowSizebroad.pda.seq.protection.TwoSampleScanSkellamPeakCallerprotected
writeResult(Collection< Annotation > windows, FileWriter writer)broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller
writeResults(Collection< Annotation > windows, String out)broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller