Inheritance diagram for broad.pda.seq.rap.CollectAnnotationEnrichments:

Collaboration diagram for broad.pda.seq.rap.CollectAnnotationEnrichments:

Classes
class	OverlapEnrichmentScore

Static Public Member Functions
static void	main (final String[] args)

Public Attributes
String	USAGE

File	INPUT

List< File >	ANNOTATIONS

String	ANALYSIS_NAME

File	OUTPUT

Integer	PERMUTATIONS = 100

boolean	KEEP_INTERMEDIATES = false

String	QUEUE = null

boolean	PERMUTE = true

String	ANNOTATION_BASE = ""

List< String >	DISCRETE_EXTENSION = new ArrayList<String>()

List< String >	BAM_EXTENSION = new ArrayList<String>()

List< String >	CONTINUOUS_EXTENSION = new ArrayList<String>()

boolean	PAIRED_END = true

Public Attributes inherited from broad.pda.seq.rap.GenomeCommandLineProgram
String	SIZES = "/seq/lincRNA/data/mm9/sizes"

String	MASK_FILE = "/seq/mguttman/ChIPData/MaskFiles/MM9Segments/all.mask.mouse.n36.d2.bin"

double	PCT_MASKED_ALLOWED = 50.0

String	REGION = null

String	GENE = null

Integer	MAX_FRAGMENT_LENGTH = 10000

Integer	MIN_MAPPING_QUALITY = 30

String	COORD_SPACE = "genomic"

String	ANNOTATION = "/seq/lincRNA/Shari/Annotations/RefSeq_LincV3_ChromatinWithNames_nonrandom_collapsed_overlappers.bed"

Protected Member Functions
String[]	customCommandLineValidation ()

int	doWork ()

void	shufflePeaks (AnnotationList< Annotation > regions, AnnotationList< Annotation > peaks, String output) throws IOException

void	submitJobs (SortedMap< String, File > annotationMap) throws IOException, InterruptedException, DrmaaException

void	calculateDiscreteAnnotationEnrichments (AnnotationList< Annotation > regions, AnnotationList< Annotation > peaks, SortedMap< String, File > discreteAnnotations) throws IOException

void	calculateBamEnrichments (AnnotationList< Annotation > regions, AnnotationList< Annotation > peaks, SortedMap< String, File > bamMap) throws IOException

void	processOneAnnotationSet (String name, AnnotationList< Annotation > regions, AnnotationList< Annotation > peaks, AnnotationCollection<?extends Annotation > annotations) throws IOException

void	collectResults (SortedMap< String, File > discreteAnnotations) throws IOException

void	cleanup (SortedMap< String, File > discreteAnnotations)

List< CountScore >	getPeakScores (AnnotationList< Annotation > regions, AnnotationList<?extends Annotation > peaks, AnnotationCollection<?extends Annotation > annotations)

Protected Member Functions inherited from broad.pda.seq.rap.GenomeCommandLineProgram
String[]	customCommandLineValidation ()

void	loadCoordinateSpace () throws IOException

CoordinateSpace	getCoordinateSpace ()

Additional Inherited Members
Public Member Functions inherited from broad.pda.seq.rap.GenomeCommandLineProgram
List< Annotation >	getRegions ()

Map< String, Annotation >	getRegionsMap ()

AnnotationList< Annotation >	getRegionSet ()

Annotation	getGenes ()

Boolean	isGenomicSpace ()

AlignmentModel	loadAlignmentModel (File bamFile)

AlignmentModel	loadAlignmentModel (File bamFile, boolean pairedEnd)

Protected Attributes inherited from broad.pda.seq.rap.GenomeCommandLineProgram
CoordinateSpace	coordinateSpace

Member Function Documentation

void broad.pda.seq.rap.CollectAnnotationEnrichments.calculateBamEnrichments	(	AnnotationList< Annotation >	regions,
		AnnotationList< Annotation >	peaks,
		SortedMap< String, File >	bamMap
	)		throws IOException

protected

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void broad.pda.seq.rap.CollectAnnotationEnrichments.calculateDiscreteAnnotationEnrichments	(	AnnotationList< Annotation >	regions,
		AnnotationList< Annotation >	peaks,
		SortedMap< String, File >	discreteAnnotations
	)		throws IOException

protected

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void broad.pda.seq.rap.CollectAnnotationEnrichments.cleanup ( SortedMap< String, File > discreteAnnotations )

protected

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void broad.pda.seq.rap.CollectAnnotationEnrichments.collectResults ( SortedMap< String, File > discreteAnnotations ) throws IOException

protected

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String [] broad.pda.seq.rap.CollectAnnotationEnrichments.customCommandLineValidation ( )

protected

int broad.pda.seq.rap.CollectAnnotationEnrichments.doWork ( )

protected

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List<CountScore> broad.pda.seq.rap.CollectAnnotationEnrichments.getPeakScores	(	AnnotationList< Annotation >	regions,
		AnnotationList<?extends Annotation >	peaks,
		AnnotationCollection<?extends Annotation >	annotations
	)

protected

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static void broad.pda.seq.rap.CollectAnnotationEnrichments.main ( final String[] args )

static

Stock main method.

Parameters

args	main arguments

void broad.pda.seq.rap.CollectAnnotationEnrichments.processOneAnnotationSet	(	String	name,
		AnnotationList< Annotation >	regions,
		AnnotationList< Annotation >	peaks,
		AnnotationCollection<?extends Annotation >	annotations
	)		throws IOException

protected

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void broad.pda.seq.rap.CollectAnnotationEnrichments.shufflePeaks	(	AnnotationList< Annotation >	regions,
		AnnotationList< Annotation >	peaks,
		String	output
	)		throws IOException

protected

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void broad.pda.seq.rap.CollectAnnotationEnrichments.submitJobs ( SortedMap< String, File > annotationMap ) throws IOException, InterruptedException, DrmaaException

protected

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Member Data Documentation

String broad.pda.seq.rap.CollectAnnotationEnrichments.ANALYSIS_NAME

String broad.pda.seq.rap.CollectAnnotationEnrichments.ANNOTATION_BASE = ""

List<File> broad.pda.seq.rap.CollectAnnotationEnrichments.ANNOTATIONS

List<String> broad.pda.seq.rap.CollectAnnotationEnrichments.BAM_EXTENSION = new ArrayList<String>()

List<String> broad.pda.seq.rap.CollectAnnotationEnrichments.CONTINUOUS_EXTENSION = new ArrayList<String>()

List<String> broad.pda.seq.rap.CollectAnnotationEnrichments.DISCRETE_EXTENSION = new ArrayList<String>()

File broad.pda.seq.rap.CollectAnnotationEnrichments.INPUT

boolean broad.pda.seq.rap.CollectAnnotationEnrichments.KEEP_INTERMEDIATES = false

File broad.pda.seq.rap.CollectAnnotationEnrichments.OUTPUT

boolean broad.pda.seq.rap.CollectAnnotationEnrichments.PAIRED_END = true

Integer broad.pda.seq.rap.CollectAnnotationEnrichments.PERMUTATIONS = 100

boolean broad.pda.seq.rap.CollectAnnotationEnrichments.PERMUTE = true

String broad.pda.seq.rap.CollectAnnotationEnrichments.QUEUE = null

String broad.pda.seq.rap.CollectAnnotationEnrichments.USAGE

Initial value:

= "Calculate overlap/count enrichments for regions in the query BED file.  " + 
                          "Significance is assessed by permuting the query BED file.  " + 
                          "Regions in the BED file can be scored against other BED files or against BAM files."

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

java/broad/pda/seq/rap/CollectAnnotationEnrichments.java

Classes

Static Public Member Functions

Public Attributes

Protected Member Functions

Additional Inherited Members

Member Function Documentation

Member Data Documentation