broad.pda.seq.protection.BatchedMultiSampleScanPeakCaller Class Reference

Inheritance diagram for broad.pda.seq.protection.BatchedMultiSampleScanPeakCaller:

Collaboration diagram for broad.pda.seq.protection.BatchedMultiSampleScanPeakCaller:

Static Public Member Functions
static String[]	extendSuperArgsForSampleAndChr (String[] commandArgs, String sampleName, String chrName)
static void	main (String[] args) throws IOException
Static Public Member Functions inherited from broad.pda.seq.protection.MultiSampleScanPeakCaller
static void	main (String[] args) throws IOException, InterruptedException, DrmaaException

Additional Inherited Members
Public Member Functions inherited from broad.pda.seq.protection.MultiSampleScanPeakCaller
	MultiSampleScanPeakCaller (String sampleListFile, String bedFile, String chrSizeFile, int window, int step) throws IOException
void	setFilterByStrand (boolean useStrandFilter)
void	setExtraFields (boolean useExtraFields)
void	setBinomialScore (boolean binomialScore)
void	setPeakCutoffMostCommonReplicate (double maxPct)
void	setPeakTrimQuantile (double trimPeakQuantile)
void	setPeakWindowCountCutoff (double peakCountCutoff)
void	setPeakWindowScanPvalCutoff (double peakScanPvalCutoff)
void	setFirstReadTranscriptionStrand (boolean firstReadIsTranscriptionStrand)
void	setExpressionScanPvalueCutoff (double expressionScanPvalCutoff)
	MultiSampleScanPeakCaller (String expressionBamFile, String signalBamFile, String bedFile, String chrSizeFile) throws IOException
	MultiSampleScanPeakCaller (String expressionBamFile, String signalBamFile, String bedFile, String chrSizeFile, int window, int step) throws IOException
boolean	isExpressedInAllControlSamples (Gene gene)
boolean	isExpressed (Gene gene)
Collection< Gene >	getSingleSampleScanPeaks (SampleData sample, Gene gene) throws IOException
Collection< Annotation >	mergePeaks (Collection< Annotation > peaks)
void	setCoordinateSpace (CoordinateSpace space)
CoordinateSpace	getCoordinateSpace ()
Protected Member Functions inherited from broad.pda.seq.protection.MultiSampleScanPeakCaller
	MultiSampleScanPeakCaller (MultiSampleScanPeakCaller other) throws IOException
void	initializeFilterRejectWriters (String commonSuffix, String outDir) throws IOException
void	closeFilterRejectWriters () throws IOException
String	getPeakBedFileName (SampleData sample, String outDir, String chrName)
void	writeSingleSampleScanPeaks (SampleData sample, String outFile, String chrName) throws IOException
SamplePermutation	getOneRandomSamplePermutation ()
void	setLoggerLevel (Level level)
Static Protected Member Functions inherited from broad.pda.seq.protection.MultiSampleScanPeakCaller
static MultiSampleScanPeakCaller	createFromCommandArgs (String[] commandArgs) throws IOException
static boolean	commandLineHasDebugFlag (String[] commandArgs)
static String	commandLineOutDir (String[] commandArgs)
Protected Attributes inherited from broad.pda.seq.protection.MultiSampleScanPeakCaller
Map< String, Collection< Gene > >	genes
Map< SampleData, Map< Gene, Map< Annotation, BinomialEnrichmentScore > > >	binomialWindowScores
GenomeSpaceSampleData	expressionData
ArrayList< SampleData >	controlSamples
ArrayList< SampleData >	signalSamples
ArrayList< SampleData >	allSamples
int	windowSize
int	stepSize
int	numControls
int	numSignals
int	numSamples
Random	random
String	sizeFile
Static Protected Attributes inherited from broad.pda.seq.protection.MultiSampleScanPeakCaller
static Logger	logger = Logger.getLogger(MultiSampleScanPeakCaller.class.getName())
static String	FILTER_REJECT_DIR = "filter_rejects"

Detailed Description

Author

prussell

Member Function Documentation

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

static

static void broad.pda.seq.protection.BatchedMultiSampleScanPeakCaller.main ( String[]  args ) throws IOException

static

Parameters

args

Exceptions

IOException

Here is the call graph for this function:

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The documentation for this class was generated from the following file:

• java/broad/pda/seq/protection/BatchedMultiSampleScanPeakCaller.java