broad.pda.seq.rap.PlotAggregateRegions Class Reference

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

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

Public Member Functions
PlotRegions	generateSubregions (Annotation region) throws IOException
Public Member Functions inherited from broad.pda.seq.rap.GenomeScoringProgram
WindowProcessor<?extends WindowScore >	getWindowProcessor ()
WindowProcessor<?extends WindowScore >	getWindowProcessor (AnnotationCollection<?extends Annotation > target, AnnotationCollection<?extends Annotation > control)
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)

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

Public Attributes
String	USAGE = "Plot scores as as a function of position from / in a target. Scans through introns in the annotation file"
File	OUTPUT
File	ANNOTATION_FILE
int	WINDOW
int	OVERLAP =0
int	INNER_LENGTH = 0
int	OUTER_LENGTH = 0
int	MIDDLE_LENGTH = 0
boolean	SYMMETRIC =false
boolean	CLIP_AT_BOUNDARIES =true
Public Attributes inherited from broad.pda.seq.rap.GenomeScoringProgram
File	TARGET
File	CONTROL = null
String	SCORE = "count"
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
void	loadCoordinateSpace ()
int	doWork ()
Protected Member Functions inherited from broad.pda.seq.rap.GenomeScoringProgram
String[]	customCommandLineValidation ()
Protected Member Functions inherited from broad.pda.seq.rap.GenomeCommandLineProgram
String[]	customCommandLineValidation ()
void	loadCoordinateSpace () throws IOException
CoordinateSpace	getCoordinateSpace ()

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

Member Function Documentation

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

protected

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PlotRegions broad.pda.seq.rap.PlotAggregateRegions.generateSubregions

(

Annotation

region

)

throws IOException

Generate subregions to scan based on the given region.

Parameters

region

Returns

Exceptions

IOException

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void broad.pda.seq.rap.PlotAggregateRegions.loadCoordinateSpace ( )

protected

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

static

Stock main method.

Parameters

args	main arguments

Member Data Documentation

File broad.pda.seq.rap.PlotAggregateRegions.ANNOTATION_FILE

boolean broad.pda.seq.rap.PlotAggregateRegions.CLIP_AT_BOUNDARIES =true

int broad.pda.seq.rap.PlotAggregateRegions.INNER_LENGTH = 0

int broad.pda.seq.rap.PlotAggregateRegions.MIDDLE_LENGTH = 0

int broad.pda.seq.rap.PlotAggregateRegions.OUTER_LENGTH = 0

File broad.pda.seq.rap.PlotAggregateRegions.OUTPUT

int broad.pda.seq.rap.PlotAggregateRegions.OVERLAP =0

boolean broad.pda.seq.rap.PlotAggregateRegions.SYMMETRIC =false

String broad.pda.seq.rap.PlotAggregateRegions.USAGE = "Plot scores as as a function of position from / in a target. Scans through introns in the annotation file"

int broad.pda.seq.rap.PlotAggregateRegions.WINDOW

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

• java/broad/pda/seq/rap/PlotAggregateRegions.java