broad.pda.seq.protection.MultiSampleScanPeakCaller Class Reference

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

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

Public Member Functions
	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 ()

Static Public Member Functions
static void	main (String[] args) throws IOException, InterruptedException, DrmaaException

Protected Member Functions
	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
static MultiSampleScanPeakCaller	createFromCommandArgs (String[] commandArgs) throws IOException
static boolean	commandLineHasDebugFlag (String[] commandArgs)
static String	commandLineOutDir (String[] commandArgs)

Protected Attributes
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
static Logger	logger = Logger.getLogger(MultiSampleScanPeakCaller.class.getName())
static String	FILTER_REJECT_DIR = "filter_rejects"

Detailed Description

Author

prussell

Constructor & Destructor Documentation

broad.pda.seq.protection.MultiSampleScanPeakCaller.MultiSampleScanPeakCaller ( MultiSampleScanPeakCaller  other ) throws IOException

protected

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broad.pda.seq.protection.MultiSampleScanPeakCaller.MultiSampleScanPeakCaller	(	String	sampleListFile,
		String	bedFile,
		String	chrSizeFile,
		int	window,
		int	step
	)		throws IOException

Instantiate using file of sample information

Parameters

sampleListFile	File containing sample list
bedFile	Bed gene annotation
chrSizeFile	Chromosome size file
window	Window size
step	Step size

Exceptions

IOException

broad.pda.seq.protection.MultiSampleScanPeakCaller.MultiSampleScanPeakCaller	(	String	expressionBamFile,
		String	signalBamFile,
		String	bedFile,
		String	chrSizeFile
	)		throws IOException

Instantiate with a single sample and an expression sample and default paramters

Parameters

expressionBamFile	Bam file for expression sample
signalBamFile	Bam file for signal sample
bedFile	Bed gene annotation
chrSizeFile	Chromosome size file

Exceptions

IOException

broad.pda.seq.protection.MultiSampleScanPeakCaller.MultiSampleScanPeakCaller	(	String	expressionBamFile,
		String	signalBamFile,
		String	bedFile,
		String	chrSizeFile,
		int	window,
		int	step
	)		throws IOException

Instantiate with a single signal sample and an expression sample

Parameters

expressionBamFile	Bam file for expression sample
signalBamFile	Bam file for signal sample
bedFile	Bed gene annotation
chrSizeFile	Chromosome size file
window	Window size
step	Step size

Exceptions

IOException

Member Function Documentation

void broad.pda.seq.protection.MultiSampleScanPeakCaller.closeFilterRejectWriters ( ) throws IOException

protected

static boolean broad.pda.seq.protection.MultiSampleScanPeakCaller.commandLineHasDebugFlag ( String[]  commandArgs )

staticprotected

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static String broad.pda.seq.protection.MultiSampleScanPeakCaller.commandLineOutDir ( String[]  commandArgs )

staticprotected

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static MultiSampleScanPeakCaller broad.pda.seq.protection.MultiSampleScanPeakCaller.createFromCommandArgs ( String[]  commandArgs ) throws IOException

staticprotected

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CoordinateSpace broad.pda.seq.protection.MultiSampleScanPeakCaller.getCoordinateSpace

(

)

SamplePermutation broad.pda.seq.protection.MultiSampleScanPeakCaller.getOneRandomSamplePermutation ( )

protected

Get a random permutation of control and signal identities

Returns

The random permutation

String broad.pda.seq.protection.MultiSampleScanPeakCaller.getPeakBedFileName ( SampleData  sample, String  outDir, String  chrName  )

protected

Get name of bed file to write for peaks

Parameters

sample	Sample
outDir	Output directory name or null if current directory
chrName	Chromosome name or null if all chromosomes

Returns

File name

Collection<Gene> broad.pda.seq.protection.MultiSampleScanPeakCaller.getSingleSampleScanPeaks	(	SampleData	sample,
		Gene	gene
	)		throws IOException

Get scan peaks for the sample and the gene

Parameters

sample	The sample
gene	The gene

Returns

Significant scan peaks

Exceptions

IOException

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void broad.pda.seq.protection.MultiSampleScanPeakCaller.initializeFilterRejectWriters ( String  commonSuffix, String  outDir  ) throws IOException

protected

boolean broad.pda.seq.protection.MultiSampleScanPeakCaller.isExpressed

(

Gene

gene

)

Whether the gene is significantly expressed in the special expression sample

Parameters

gene

The gene

Returns

True iff the gene is expressed in the expression sample

boolean broad.pda.seq.protection.MultiSampleScanPeakCaller.isExpressedInAllControlSamples

(

Gene

gene

)

Whether the gene is expressed in all control samples at the given significance level

Parameters

gene

The gene

Returns

Whether the gene is expressed by these criteria

static void broad.pda.seq.protection.MultiSampleScanPeakCaller.main ( String[]  args ) throws IOException, InterruptedException, DrmaaException

static

Parameters

args

Exceptions

IOException
InterruptedException
DrmaaException

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Collection<Annotation> broad.pda.seq.protection.MultiSampleScanPeakCaller.mergePeaks

(

Collection< Annotation >

peaks

)

void broad.pda.seq.protection.MultiSampleScanPeakCaller.setBinomialScore

(

boolean

binomialScore

)

Set whether to print extra fields

Parameters

useExtraFields

void broad.pda.seq.protection.MultiSampleScanPeakCaller.setCoordinateSpace

(

CoordinateSpace

space

)

void broad.pda.seq.protection.MultiSampleScanPeakCaller.setExpressionScanPvalueCutoff

(

double

expressionScanPvalCutoff

)

Set genome wide scan P value cutoff for expression of transcript

Parameters

expressionScanPvalCutoff

P value cutoff for transcript expression against genomic background

void broad.pda.seq.protection.MultiSampleScanPeakCaller.setExtraFields

(

boolean

useExtraFields

)

Set whether to print extra fields

Parameters

useExtraFields

void broad.pda.seq.protection.MultiSampleScanPeakCaller.setFilterByStrand

(

boolean

useStrandFilter

)

Set whether to use strand information in reads to filter peaks

Parameters

useStrandFilter

Whether to apply strand filter

void broad.pda.seq.protection.MultiSampleScanPeakCaller.setFirstReadTranscriptionStrand

(

boolean

firstReadIsTranscriptionStrand

)

Set whether read 1 is transcription strand

Parameters

firstReadIsTranscriptionStrand

True if read 1 is transcription strand

void broad.pda.seq.protection.MultiSampleScanPeakCaller.setLoggerLevel ( Level  level )

protected

Set logger levels for all samples

Parameters

level

Level

void broad.pda.seq.protection.MultiSampleScanPeakCaller.setPeakCutoffMostCommonReplicate

(

double

maxPct

)

Set cutoff for the percentage of fragments overlapping a peak that come from the most common replicate fragment

Parameters

maxPct

The max percentage

void broad.pda.seq.protection.MultiSampleScanPeakCaller.setPeakTrimQuantile

(

double

trimPeakQuantile

)

Set quantile for trim max contiguous algorithm for peak calling

Parameters

trimPeakQuantile

The quantile of data values

void broad.pda.seq.protection.MultiSampleScanPeakCaller.setPeakWindowCountCutoff

(

double

peakCountCutoff

)

Set minimum number of fragments overlapping a window to be considered for possible peak

Parameters

peakCountCutoff

Minimum fragment count for each window

void broad.pda.seq.protection.MultiSampleScanPeakCaller.setPeakWindowScanPvalCutoff

(

double

peakScanPvalCutoff

)

Set scan P value cutoff for window within transcript to be considered for possible peak

Parameters

peakScanPvalCutoff

Max scan P value

void broad.pda.seq.protection.MultiSampleScanPeakCaller.writeSingleSampleScanPeaks ( SampleData  sample, String  outFile, String  chrName  ) throws IOException

protected

Write all single sample scan peaks for the sample and chromosome to file

Parameters

sample	The sample
outFile	Output bed file
r	Red value for bed file color
g	Green value for bed file color
b	Blue value for bed file color
chrName	Only write peaks for this chromosome

Exceptions

IOException

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Member Data Documentation

ArrayList<SampleData> broad.pda.seq.protection.MultiSampleScanPeakCaller.allSamples

protected

Map<SampleData, Map<Gene, Map<Annotation, BinomialEnrichmentScore> > > broad.pda.seq.protection.MultiSampleScanPeakCaller.binomialWindowScores

protected

ArrayList<SampleData> broad.pda.seq.protection.MultiSampleScanPeakCaller.controlSamples

protected

GenomeSpaceSampleData broad.pda.seq.protection.MultiSampleScanPeakCaller.expressionData

protected

String broad.pda.seq.protection.MultiSampleScanPeakCaller.FILTER_REJECT_DIR = "filter_rejects"

staticprotected

Map<String, Collection<Gene> > broad.pda.seq.protection.MultiSampleScanPeakCaller.genes

protected

Logger broad.pda.seq.protection.MultiSampleScanPeakCaller.logger = Logger.getLogger(MultiSampleScanPeakCaller.class.getName())

staticprotected

int broad.pda.seq.protection.MultiSampleScanPeakCaller.numControls

protected

int broad.pda.seq.protection.MultiSampleScanPeakCaller.numSamples

protected

int broad.pda.seq.protection.MultiSampleScanPeakCaller.numSignals

protected

Random broad.pda.seq.protection.MultiSampleScanPeakCaller.random

protected

ArrayList<SampleData> broad.pda.seq.protection.MultiSampleScanPeakCaller.signalSamples

protected

String broad.pda.seq.protection.MultiSampleScanPeakCaller.sizeFile

protected

int broad.pda.seq.protection.MultiSampleScanPeakCaller.stepSize

protected

int broad.pda.seq.protection.MultiSampleScanPeakCaller.windowSize

protected

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

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