Static Public Member Functions
static Map< String, Map< Gene, Collection< Gene > > >	mapGenesToOverlappers (Map< String, Collection< Gene >> genes, Map< String, Collection< Gene >> intersectSet)

static Map< String, Collection < Gene > >	getOverlap (Map< String, Collection< Gene >> genes, Map< String, Collection< Gene >> intersectSet)

static Map< String, Collection < Gene > >	getOverlap (Map< String, Collection< Gene >> genes, Map< String, Collection< Gene >> intersectSet, boolean verbose)

static Map< String, Collection < Gene > >	getOverlap (Map< String, Collection< Gene >> genes, Map< String, Collection< Gene >> intersectSet, Map< String, Collection< Gene >> excludeSet)

static Map< String, Collection < Gene > >	getOverlap (Map< String, Collection< Gene >> genes, Map< String, Collection< Gene >> intersectSet, Map< String, Collection< Gene >> excludeSet, boolean verbose)

static int	countOverlappers (Map< String, Collection< Gene >> regionsToCount, Map< String, Collection< Gene >> regionsToOverlapWith)

static int	countOverlappers (Map< String, Collection< Gene >> regionsToCount, Map< String, Collection< Gene >> regionsToOverlapWith, Map< String, Collection< Gene >> excludeSet)

static Map< String, Collection < Gene > >	getOverlapWithRandomizedPositions (Map< String, Collection< Gene >> regions, Map< String, Collection< Gene >> intersectGenes)

static Map< String, Collection < Gene > >	getOverlapWithRandomizedPositions (Map< String, Collection< Gene >> regions, Map< String, Collection< Gene >> intersectGenes, Map< String, Collection< Gene >> excludeFeatures)

static int	numOverlappingBases (Map< String, Collection< Gene >> genes, Map< String, Collection< Gene >> intersectSet)

static int	numOverlappingBases (Map< String, Collection< Gene >> genes, Map< String, Collection< Gene >> intersectSet, Map< String, Collection< Gene >> excludeSet)

static int	numOverlappingGenes (Map< String, Collection< Gene >> genes, Map< String, Collection< Gene >> intersectSet)

static int	numOverlappingGenes (Map< String, Collection< Gene >> genes, Map< String, Collection< Gene >> intersectSet, Map< String, Collection< Gene >> excludeGenes)

static void	writeOverlap (String geneFile, String intersectFile, String outFile, boolean randomizePositionsWithinEachGene) throws IOException

static void	writeOverlap (String geneFile, String intersectFile, String excludeFile, String outFile, boolean randomizePositionsWithinEachGene) throws IOException

static void	writeOverlap (Map< String, Collection< Gene >> genes, Map< String, Collection< Gene >> intersectSet, String outFile, boolean randomizePositionsWithinEachGene) throws IOException

static void	writeOverlap (Map< String, Collection< Gene >> genes, Map< String, Collection< Gene >> intersectSet, Map< String, Collection< Gene >> excludeSet, String outFile, boolean randomizePositionsWithinEachGene) throws IOException

static void	writeGeneralStats (String geneFile, String intersectFile1, String intersectFile2, String excludeFile, String outFile) throws IOException

static void	main (String[] args) throws IOException

Detailed Description

Author: prussell

Member Function Documentation

static int broad.core.overlaputils.GeneSetIntersect.countOverlappers	(	Map< String, Collection< Gene >>	regionsToCount,
		Map< String, Collection< Gene >>	regionsToOverlapWith
	)

static

Count number of regions that overlap at least one region in other set

Parameters

regionsToCount	Regions to count
regionsToOverlapWith	Potential overlappers

Returns: The number of regions in the first set that overlap at least one region in other set

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static int broad.core.overlaputils.GeneSetIntersect.countOverlappers	(	Map< String, Collection< Gene >>	regionsToCount,
		Map< String, Collection< Gene >>	regionsToOverlapWith,
		Map< String, Collection< Gene >>	excludeSet
	)

static

Count number of regions that overlap at least one region in other set

Parameters

regionsToCount	Regions to count
regionsToOverlapWith	Potential overlappers
excludeSet	Exclude regions from first set if they overlap a region in this set

Returns: The number of regions in the first set that overlap at least one region in other set

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static Map<String, Collection<Gene> > broad.core.overlaputils.GeneSetIntersect.getOverlap	(	Map< String, Collection< Gene >>	genes,
		Map< String, Collection< Gene >>	intersectSet
	)

static

Get overlap between two gene sets

Parameters

genes	Genes by chromosome
intersectSet	Set to intersect with by chromosome

Returns: Set of Gene objects representing the overlaps

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static Map<String, Collection<Gene> > broad.core.overlaputils.GeneSetIntersect.getOverlap	(	Map< String, Collection< Gene >>	genes,
		Map< String, Collection< Gene >>	intersectSet,
		boolean	verbose
	)

static

Get overlap between two gene sets

Parameters

genes	Genes by chromosome
intersectSet	Set to intersect with by chromosome
verbose	Print messages

Returns: Set of Gene objects representing the overlaps

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static Map<String, Collection<Gene> > broad.core.overlaputils.GeneSetIntersect.getOverlap	(	Map< String, Collection< Gene >>	genes,
		Map< String, Collection< Gene >>	intersectSet,
		Map< String, Collection< Gene >>	excludeSet
	)

static

Get overlap between two gene sets and automatically exclude all genes in a set

Parameters

genes	Genes by chromosome
intersectSet	Set to intersect with by chromosome
excludeSet	Exclude genes if they overlap a region from this set

Returns: Set of Gene objects representing the overlaps

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static Map<String, Collection<Gene> > broad.core.overlaputils.GeneSetIntersect.getOverlap	(	Map< String, Collection< Gene >>	genes,
		Map< String, Collection< Gene >>	intersectSet,
		Map< String, Collection< Gene >>	excludeSet,
		boolean	verbose
	)

static

Get overlap between two gene sets and automatically exclude all genes in a set

Parameters

genes	Genes by chromosome
intersectSet	Set to intersect with by chromosome
excludeSet	Exclude genes from first gene set if they overlap a gene from this set
verbose	Print messages

Returns: Set of Gene objects representing the overlaps

static Map<String, Collection<Gene> > broad.core.overlaputils.GeneSetIntersect.getOverlapWithRandomizedPositions	(	Map< String, Collection< Gene >>	regions,
		Map< String, Collection< Gene >>	intersectGenes
	)

static

Intersect a set of regions with another set of genes and randomize positions of the regions within each gene

Parameters

regions	The regions of interest
intersectGenes	The genes to intersect with and randomize within

Returns: Regions that have been intersected with the gene set and then randomized within each intersect gene

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static Map<String, Collection<Gene> > broad.core.overlaputils.GeneSetIntersect.getOverlapWithRandomizedPositions	(	Map< String, Collection< Gene >>	regions,
		Map< String, Collection< Gene >>	intersectGenes,
		Map< String, Collection< Gene >>	excludeFeatures
	)

static

Intersect a set of regions with another set of genes and randomize positions of the regions within each gene

Parameters

regions	The regions of interest
intersectGenes	The genes to intersect with and randomize within
excludeFeatures	Do not consider features that overlap one of these

Returns: Regions that have been intersected with the gene set and then randomized within each intersect gene

static void broad.core.overlaputils.GeneSetIntersect.main ( String[] args ) throws IOException

static

Parameters

args

Exceptions

IOException

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static Map<String, Map<Gene, Collection<Gene> > > broad.core.overlaputils.GeneSetIntersect.mapGenesToOverlappers	(	Map< String, Collection< Gene >>	genes,
		Map< String, Collection< Gene >>	intersectSet
	)

static

Map each gene to the collection of overlappers in another set

Parameters

genes	The genes by chromosome
intersectSet	The other set by chromosome

Returns: By chromosome: map of each gene that has overlappers in the other set to its overlappers

static int broad.core.overlaputils.GeneSetIntersect.numOverlappingBases	(	Map< String, Collection< Gene >>	genes,
		Map< String, Collection< Gene >>	intersectSet
	)

static

Get number of overlapping bases between two gene sets

Parameters

genes	Genes by chromosome
intersectSet	Set to intersect with by chromosome

Returns: The total number of overlapping bases

static int broad.core.overlaputils.GeneSetIntersect.numOverlappingBases	(	Map< String, Collection< Gene >>	genes,
		Map< String, Collection< Gene >>	intersectSet,
		Map< String, Collection< Gene >>	excludeSet
	)

static

Get number of overlapping bases between two gene sets and automatically exclude all genes in a set

Parameters

genes	Genes by chromosome
intersectSet	Set to intersect with by chromosome
excludeSet	Exclude genes if they overlap a gene from this set

Returns: The total number of overlapping bases

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static int broad.core.overlaputils.GeneSetIntersect.numOverlappingGenes	(	Map< String, Collection< Gene >>	genes,
		Map< String, Collection< Gene >>	intersectSet
	)

static

Get number of overlapping genes between two gene sets

Parameters

genes	Genes by chromosome
intersectSet	Set to intersect with by chromosome

Returns: The total number of overlapping bases

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static int broad.core.overlaputils.GeneSetIntersect.numOverlappingGenes	(	Map< String, Collection< Gene >>	genes,
		Map< String, Collection< Gene >>	intersectSet,
		Map< String, Collection< Gene >>	excludeGenes
	)

static

Get number of overlapping genes between two gene sets and automatically exclude all genes in a set

Parameters

genes	Genes by chromosome
intersectSet	Set to intersect with by chromosome
excludeGenes	Exclude genes from first gene set if they overlap a gene from this set

Returns: The total number of overlapping bases

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static void broad.core.overlaputils.GeneSetIntersect.writeGeneralStats	(	String	geneFile,
		String	intersectFile1,
		String	intersectFile2,
		String	excludeFile,
		String	outFile
	)		throws IOException

static

Write basic overlap stats to a file

Parameters

geneFile	Gene bed file
intersectFile1	Intersect set 1 bed file
intersectFile2	Intersect set 2 bed file
excludeFile	Exclude genes if they overlap a gene in this bed file
outFile	Output file of stats

Exceptions

IOException

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static void broad.core.overlaputils.GeneSetIntersect.writeOverlap	(	String	geneFile,
		String	intersectFile,
		String	outFile,
		boolean	randomizePositionsWithinEachGene
	)		throws IOException

static

Get overlap between two gene sets specified in bed files and write to a file

Parameters

geneFile	Bed file of genes
intersectFile	Bed file of regions to intersect with
outFile	Output bed file to write genes representing the overlaps
randomizePositionsWithinEachGene	Whether to randomize the position of each overlap within the gene

Exceptions

IOException

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static void broad.core.overlaputils.GeneSetIntersect.writeOverlap	(	String	geneFile,
		String	intersectFile,
		String	excludeFile,
		String	outFile,
		boolean	randomizePositionsWithinEachGene
	)		throws IOException

static

Get overlap between two gene sets specified in bed files, automatically excluding all genes in a set, and write to a file

Parameters

geneFile	Bed file of genes
intersectFile	Bed file of regions to intersect with
excludeFile	Exclude genes if they overlap a gene from this set
outFile	Output bed file to write Genes representing the overlaps
randomizePositionsWithinEachGene	Whether to randomize the position of each overlap within the gene

Exceptions

IOException

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static void broad.core.overlaputils.GeneSetIntersect.writeOverlap	(	Map< String, Collection< Gene >>	genes,
		Map< String, Collection< Gene >>	intersectSet,
		String	outFile,
		boolean	randomizePositionsWithinEachGene
	)		throws IOException

static

Get overlap between two gene sets and write to a file

Parameters

genes	Genes by chromosome
intersectSet	Set to intersect with by chromosome
outFile	Output bed file to write Genes representing the overlaps
randomizePositionsWithinEachGene	Whether to randomize the position of each overlap within the gene

Exceptions

IOException

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static void broad.core.overlaputils.GeneSetIntersect.writeOverlap	(	Map< String, Collection< Gene >>	genes,
		Map< String, Collection< Gene >>	intersectSet,
		Map< String, Collection< Gene >>	excludeSet,
		String	outFile,
		boolean	randomizePositionsWithinEachGene
	)		throws IOException

static

Get overlap between two gene sets, automatically excluding all genes in a set, and write to a file

Parameters

genes	Genes by chromosome
intersectSet	Set to intersect with by chromosome
excludeSet	Exclude genes if they overlap a gene from this set
outFile	Output bed file to write Genes representing the overlaps
randomizePositionsWithinEachGene	Whether to randomize the position of each overlap within the gene

Exceptions

IOException

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

java/broad/core/overlaputils/GeneSetIntersect.java

Static Public Member Functions

Detailed Description

Member Function Documentation