GenomicInteractions-package	GenomicInteractions-package
.importHicLib	dot-importHicLib
.importHomer	dot-importHomer
.processChiapetName	dot-processChiapetName
.readBam	dot-readBam
.readTwoBams	dot-readTwoBams
.validateInput	dot-validateInput
anchorOne	getters
anchorOne,GInteractions-method	getters
anchorTwo	getters
anchorTwo,GInteractions-method	getters
annotateInteractions	annotateInteractions
annotateInteractions,GInteractions,list-method	annotateInteractions
annotateRegions	annotateRegions
annotateRegions,GInteractions,character,vector-method	annotateRegions
annotationFeatures	getters
annotationFeatures,GInteractions-method	getters
asBED,GInteractions-method	asBED-GInteractions-method
availableDisplayPars	availableDisplayPars
calculateDistances	calculateDistances
calculateDistances,GInteractions-method	calculateDistances
categoriseInteractions	categoriseInteractions
chromosome,InteractionTrack-method	InteractionTrack-class
countsBetweenAnchors	countsBetweenAnchors-methods
countsBetweenAnchors,GInteractions,GRanges-method	countsBetweenAnchors-methods
description,GInteractions-method	getters
description<-,GInteractions,ANY-method	setters
end,InteractionTrack-method	InteractionTrack-class
export.bed12	export.bed12
export.bed12,GInteractions-method	export.bed12
export.bedpe	export.bedpe
export.bedpe,GInteractions-method	export.bedpe
export.chiasig	export.chiasig
export.chiasig,GInteractions-method	export.chiasig
export.igraph	export.igraph
export.igraph,GInteractions-method	export.igraph
GenomicInteractions	GenomicInteractions
GenomicInteractions,ANY,ANY,ANY-method	GenomicInteractions
GenomicInteractions,GInteractions,ANY,ANY-method	GenomicInteractions
GenomicInteractions,GInteractions,numeric,ANY-method	GenomicInteractions
GenomicInteractions,GRanges,GRanges,GenomicRanges_OR_missing-method	GenomicInteractions
GenomicInteractions,GRanges,GRanges,numeric-method	GenomicInteractions
GenomicInteractions,missing,missing,GenomicRanges_OR_missing-method	GenomicInteractions
GenomicInteractions,numeric,numeric,GRanges-method	GenomicInteractions
GenomicInteractions-class	GenomicInteractions-class
getters	getters
get_binom_ligation_threshold	get_binom_ligation_threshold
get_self_ligation_threshold	get_self_ligation_threshold
hg19.refseq.transcripts	hg19.refseq.transcripts
hic_example_data	hic_example_data
interactionCounts	getters
interactionCounts,GInteractions-method	getters
interactionCounts<-	setters
interactionCounts<-,GInteractions-method	setters
InteractionHelpers	InteractionHelpers
InteractionTrack	InteractionTrack
InteractionTrack-class	InteractionTrack-class
is.cis	InteractionHelpers
is.cis,GInteractions-method	InteractionHelpers
is.dd	InteractionHelpers
is.dd,GInteractions-method	InteractionHelpers
is.dt	InteractionHelpers
is.dt,GInteractions-method	InteractionHelpers
is.pd	InteractionHelpers
is.pd,GInteractions-method	InteractionHelpers
is.pp	InteractionHelpers
is.pp,GInteractions-method	InteractionHelpers
is.pt	InteractionHelpers
is.pt,GInteractions-method	InteractionHelpers
is.trans	InteractionHelpers
is.trans,GInteractions-method	InteractionHelpers
is.tt	InteractionHelpers
is.tt,GInteractions-method	InteractionHelpers
isInteractionType	InteractionHelpers
isInteractionType,GInteractions-method	InteractionHelpers
makeGenomicInteractionsFromFile	makeGenomicInteractionsFromFile
mm9_refseq_promoters	mm9_refseq_promoters
name	getters
name,GInteractions-method	getters
name<-	setters
name<-,GInteractions-method	setters
plotAvgViewpoint	plotAvgViewpoint
plotCisTrans	plotCisTrans
plotCounts	plotCounts
plotDists	plotDists
plotInteractionAnnotations	plotInteractionAnnotations
plotSummaryStats	plotSummaryStats
plotViewpoint	plotViewpoint
removeDups	removeDups
resetAnnotations	resetAnnotations
resetAnnotations,GInteractions-method	resetAnnotations
sameStrand	sameStrand
setters	setters
start,InteractionTrack-method	InteractionTrack-class
subset,InteractionTrack-method	InteractionTrack-class
subsetByFeatures	GInteractions-subsetByFeatures-methods
subsetByFeatures,GInteractions,character,character-method	GInteractions-subsetByFeatures-methods
subsetByFeatures,GInteractions,GRanges,missing-method	GInteractions-subsetByFeatures-methods
subsetByFeatures,GInteractions,GRangesList,missing-method	GInteractions-subsetByFeatures-methods
sum,GInteractions-method	sum-GInteractions-method
summariseByFeaturePairs	summariseByFeaturePairs
summariseByFeaturePairs,GInteractions-method	summariseByFeaturePairs
summariseByFeatures	summariseByFeatures
summariseByFeatures,GInteractions-method	summariseByFeatures
thymus_enh	thymus_enh
updateObject,GenomicInteractions-method	updateObject-GenomicInteractions-method
viewPoint	viewPoint
