GenomicInteractions-package	GenomicInteractions-package
$,GenomicInteractions-method	GenomicInteractions-dollar-methods
$<-,GenomicInteractions-method	GenomicInteractions-dollar-methods
anchorOne	getters
anchorOne,GenomicInteractions-method	getters
anchorTwo	getters
anchorTwo,GenomicInteractions-method	getters
annotateAnchors	annotateAnchors
annotateAnchors,GenomicInteractions,numeric,character,vector-method	annotateAnchors
annotateInteractions	annotateInteractions
annotateInteractions,GenomicInteractions,list-method	annotateInteractions
annotationFeatures	getters
annotationFeatures,GenomicInteractions-method	getters
c	GenomicInteractions-combine-methods
c,GenomicInteractions-method	GenomicInteractions-combine-methods
calculateDistances	calculateDistances
calculateDistances,GenomicInteractions-method	calculateDistances
capitalize	capitalize
categoriseInteractions	categoriseInteractions
countOverlaps,GenomicInteractions,GRanges-method	GenomicInteractions-overlaps-methods
countOverlaps,GRanges,GenomicInteractions-method	GenomicInteractions-overlaps-methods
countsBetweenAnchors	countsBetweenAnchors-methods
countsBetweenAnchors,GenomicInteractions,GRanges-method	countsBetweenAnchors-methods
description	getters
description,GenomicInteractions-method	getters
description<-	setters
description<-,GenomicInteractions-method	setters
export.bed12	export.bed12
export.bed12,GenomicInteractions-method	export.bed12
export.bedpe	export.bedpe
export.bedpe,GenomicInteractions-method	export.bedpe
export.chiasig	export.chiasig
export.chiasig,GenomicInteractions-method	export.chiasig
export.igraph	export.igraph
export.igraph,GenomicInteractions-method	export.igraph
findOverlaps	GenomicInteractions-overlaps-methods
findOverlaps,GenomicInteractions,GenomicInteractions-method	GenomicInteractions-overlaps-methods
findOverlaps,GenomicInteractions,GRanges-method	GenomicInteractions-overlaps-methods
findOverlaps,GRanges,GenomicInteractions-method	GenomicInteractions-overlaps-methods
GenomicInteractions	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,GenomicInteractions-method	getters
interactionCounts<-	setters
interactionCounts<-,GenomicInteractions-method	setters
InteractionHelpers	InteractionHelpers
is.cis	InteractionHelpers
is.cis,GenomicInteractions-method	InteractionHelpers
is.dd	InteractionHelpers
is.dd,GenomicInteractions-method	InteractionHelpers
is.dt	InteractionHelpers
is.dt,GenomicInteractions-method	InteractionHelpers
is.pd	InteractionHelpers
is.pd,GenomicInteractions-method	InteractionHelpers
is.pp	InteractionHelpers
is.pp,GenomicInteractions-method	InteractionHelpers
is.pt	InteractionHelpers
is.pt,GenomicInteractions-method	InteractionHelpers
is.trans	InteractionHelpers
is.trans,GenomicInteractions-method	InteractionHelpers
is.tt	InteractionHelpers
is.tt,GenomicInteractions-method	InteractionHelpers
isInteractionType	InteractionHelpers
isInteractionType,GenomicInteractions-method	InteractionHelpers
length,GenomicInteractions-method	length-GenomicInteractions-method
makeGenomicInteractionsFromFile	makeGenomicInteractionsFromFile
mm9_refseq_promoters	mm9_refseq_promoters
name	getters
name,GenomicInteractions-method	getters
name<-	setters
name<-,GenomicInteractions-method	setters
overlapsAny,GenomicInteractions,GRanges-method	GenomicInteractions-overlaps-methods
overlapsAny,GRanges,GenomicInteractions-method	GenomicInteractions-overlaps-methods
plotCisTrans	plotCisTrans
plotCounts	plotCounts
plotDists	plotDists
plotInteractionAnnotations	plotInteractionAnnotations
plotSummaryStats	plotSummaryStats
plotViewpoint	plotViewpoint
print,GenomicInteractions-method	print-GenomicInteractions-method
removeDups	removeDups
resetAnnotations	resetAnnotations
resetAnnotations,GenomicInteractions-method	resetAnnotations
sameStrand	sameStrand
seqinfo,GenomicInteractions-method	seqinfo-GenomicInteractions-method
seqinfo<-,GenomicInteractions-method	seqinfo-GenomicInteractions-method
setters	setters
show,GenomicInteractions-method	show-GenomicInteractions-method
sort,GenomicInteractions-method	sort-GenomicInteractions-method
subsetByFeatures	GenomicInteractions-subsetByFeatures-methods
subsetByFeatures,GenomicInteractions,character,character-method	GenomicInteractions-subsetByFeatures-methods
subsetByFeatures,GenomicInteractions,GRanges,missing-method	GenomicInteractions-subsetByFeatures-methods
subsetByFeatures,GenomicInteractions,GRangesList,missing-method	GenomicInteractions-subsetByFeatures-methods
sum,GenomicInteractions-method	sum-GenomicInteractions-method
summariseByFeatures	summariseByFeatures
summariseByFeatures,GenomicInteractions-method	summariseByFeatures
trim,GenomicInteractions-method	trim-GenomicInteractions-method
viewPoint	viewPoint
[	GenomicInteractions-subset-methods
[,GenomicInteractions,ANY,ANY-method	GenomicInteractions-subset-methods
