$,GInteractions-method	interaction-accessors
$<-,GInteractions-method	interaction-accessors
anchorIds	interaction-accessors
anchorIds,ContactMatrix-method	ContactMatrix-accessors
anchorIds,GInteractions-method	interaction-accessors
anchorIds,InteractionSet-method	interaction-accessors
anchorIds<-	interaction-accessors
anchorIds<-,ContactMatrix-method	ContactMatrix-accessors
anchorIds<-,GInteractions-method	interaction-accessors
anchorIds<-,InteractionSet-method	interaction-accessors
anchorIds<-,ReverseStrictGInteractions-method	interaction-accessors
anchorIds<-,StrictGInteractions-method	interaction-accessors
anchors	interaction-accessors
anchors,ContactMatrix-method	ContactMatrix-accessors
anchors,GInteractions-method	interaction-accessors
anchors,InteractionSet-method	interaction-accessors
anchors<-	interaction-accessors
anchors<-,ContactMatrix-method	ContactMatrix-accessors
anchors<-,GInteractions-method	interaction-accessors
anchors<-,InteractionSet-method	interaction-accessors
anchors<-,ReverseStrictGInteractions-method	interaction-accessors
anchors<-,StrictGInteractions-method	interaction-accessors
appendRegions<-	interaction-accessors
appendRegions<-,ContactMatrix-method	ContactMatrix-accessors
appendRegions<-,GInteractions-method	interaction-accessors
appendRegions<-,InteractionSet-method	interaction-accessors
as.data.frame,GInteractions-method	interaction-accessors
as.matrix,ContactMatrix-method	ContactMatrix-accessors
as.matrix<-	ContactMatrix-accessors
as.matrix<-,ContactMatrix-method	ContactMatrix-accessors
boundingBox	boundingBox
boundingBox,GInteractions-method	boundingBox
boundingBox,InteractionSet-method	boundingBox
c,GInteractions-method	interaction-bind
cbind,ContactMatrix-method	ContactMatrix-subset
cbind,InteractionSet-method	interaction-bind
ContactMatrix	ContactMatrix-class
ContactMatrix,ANY,GRanges,GRanges,GenomicRanges_OR_missing-method	ContactMatrix-class
ContactMatrix,ANY,numeric,numeric,GRanges-method	ContactMatrix-class
ContactMatrix,missing,missing,missing,GenomicRanges_OR_missing-method	ContactMatrix-class
ContactMatrix-access	ContactMatrix-accessors
ContactMatrix-class	ContactMatrix-class
ContactMatrix-dist	ContactMatrix-distances
ContactMatrix-sort	ContactMatrix-sorting
ContactMatrix-subset	ContactMatrix-subset
countOverlaps	overlaps
countOverlaps,GInteractions,GInteractions-method	overlaps
countOverlaps,GInteractions,InteractionSet-method	overlaps
countOverlaps,GInteractions,missing-method	overlaps
countOverlaps,GInteractions,Vector-method	overlaps
countOverlaps,InteractionSet,GInteractions-method	overlaps
countOverlaps,InteractionSet,InteractionSet-method	overlaps
countOverlaps,InteractionSet,missing-method	overlaps
countOverlaps,InteractionSet,Vector-method	overlaps
countOverlaps,Vector,GInteractions-method	overlaps
countOverlaps,Vector,InteractionSet-method	overlaps
deflate	conversion
deflate,ContactMatrix-method	conversion
dim,ContactMatrix-method	ContactMatrix-accessors
dimnames,ContactMatrix-method	ContactMatrix-accessors
dimnames<-,ContactMatrix,ANY-method	ContactMatrix-accessors
dimnames<-,ContactMatrix-method	ContactMatrix-accessors
duplicated,ContactMatrix-method	ContactMatrix-sorting
duplicated,GInteractions-method	interaction-compare
duplicated,InteractionSet-method	interaction-compare
findOverlaps	overlaps
findOverlaps,GInteractions,GInteractions-method	overlaps
findOverlaps,GInteractions,InteractionSet-method	overlaps
findOverlaps,GInteractions,missing-method	overlaps
findOverlaps,GInteractions,Vector-method	overlaps
findOverlaps,InteractionSet,GInteractions-method	overlaps
findOverlaps,InteractionSet,InteractionSet-method	overlaps
findOverlaps,InteractionSet,missing-method	overlaps
findOverlaps,InteractionSet,Vector-method	overlaps
findOverlaps,Vector,GInteractions-method	overlaps
findOverlaps,Vector,InteractionSet-method	overlaps
first	interaction-accessors
first,GInteractions-method	interaction-accessors
first,InteractionSet-method	interaction-accessors
flank,ContactMatrix-method	granges-methods
flank,GInteractions-method	granges-methods
flank,InteractionSet-method	granges-methods
GInteractions	GInteractions-class
GInteractions,GRanges,GRanges,GenomicRanges_OR_missing-method	GInteractions-class
GInteractions,missing,missing,GenomicRanges_OR_missing-method	GInteractions-class
GInteractions,numeric,numeric,GRanges-method	GInteractions-class
GInteractions-class	GInteractions-class
inflate	conversion
inflate,GInteractions-method	conversion
inflate,InteractionSet-method	conversion
interaction-access	interaction-accessors
interaction-bind	interaction-bind
interaction-compare	interaction-compare
Interaction-overlaps	overlaps
interaction-subset	interaction-subset
interactions	interaction-accessors
interactions,InteractionSet-method	interaction-accessors
interactions<-	interaction-accessors
interactions<-,InteractionSet-method	interaction-accessors
InteractionSet	InteractionSet-class
InteractionSet,ANY,GInteractions-method	InteractionSet-class
InteractionSet,missing,missing-method	InteractionSet-class
InteractionSet-class	InteractionSet-class
intrachr	distances
intrachr,ContactMatrix-method	ContactMatrix-distances
intrachr,GInteractions-method	distances
intrachr,InteractionSet-method	distances
length,ContactMatrix-method	ContactMatrix-accessors
length,GInteractions-method	interaction-accessors
linearize	linearize
linearize,GInteractions,GRanges-method	linearize
linearize,GInteractions,numeric-method	linearize
linearize,InteractionSet,GRanges-method	linearize
linearize,InteractionSet,numeric-method	linearize
linkOverlaps	linkOverlaps
linkOverlaps,GInteractions,Hits,Hits-method	linkOverlaps
linkOverlaps,GInteractions,Hits,missing-method	linkOverlaps
linkOverlaps,GInteractions,Vector,missing-method	linkOverlaps
linkOverlaps,GInteractions,Vector,Vector-method	linkOverlaps
linkOverlaps,InteractionSet,Hits,Hits-method	linkOverlaps
linkOverlaps,InteractionSet,Hits,missing-method	linkOverlaps
linkOverlaps,InteractionSet,Vector,missing-method	linkOverlaps
linkOverlaps,InteractionSet,Vector,Vector-method	linkOverlaps
makeGInteractionsFromGRangesPairs	pairs
match,GInteractions,GInteractions-method	interaction-compare
match,GInteractions,InteractionSet-method	interaction-compare
match,InteractionSet,GInteractions-method	interaction-compare
match,InteractionSet,InteractionSet-method	interaction-compare
mcols,InteractionSet-method	interaction-accessors
mcols<-,InteractionSet-method	interaction-accessors
names,GInteractions-method	interaction-accessors
names,InteractionSet-method	interaction-accessors
names<-,GInteractions-method	interaction-accessors
names<-,InteractionSet-method	interaction-accessors
narrow,ContactMatrix-method	granges-methods
narrow,GInteractions-method	granges-methods
narrow,InteractionSet-method	granges-methods
order,ContactMatrix-method	ContactMatrix-sorting
order,GInteractions-method	interaction-compare
order,InteractionSet-method	interaction-compare
overlapsAny	overlaps
overlapsAny,ContactMatrix,GInteractions-method	ContactMatrix-overlaps
overlapsAny,ContactMatrix,GRanges-method	ContactMatrix-overlaps
overlapsAny,ContactMatrix,GRangesList-method	ContactMatrix-overlaps
overlapsAny,ContactMatrix,InteractionSet-method	ContactMatrix-overlaps
overlapsAny,GInteractions,GInteractions-method	overlaps
overlapsAny,GInteractions,InteractionSet-method	overlaps
overlapsAny,GInteractions,missing-method	overlaps
overlapsAny,GInteractions,Vector-method	overlaps
overlapsAny,InteractionSet,GInteractions-method	overlaps
overlapsAny,InteractionSet,InteractionSet-method	overlaps
overlapsAny,InteractionSet,missing-method	overlaps
overlapsAny,InteractionSet,Vector-method	overlaps
overlapsAny,Vector,GInteractions-method	overlaps
overlapsAny,Vector,InteractionSet-method	overlaps
pairdist	distances
pairdist,ContactMatrix-method	ContactMatrix-distances
pairdist,GInteractions-method	distances
pairdist,InteractionSet-method	distances
pairs	pairs
pairs,GInteractions-method	pairs
pairs,InteractionSet-method	pairs
pcompare,GInteractions,GInteractions-method	interaction-compare
rbind,ContactMatrix-method	ContactMatrix-subset
rbind,InteractionSet-method	interaction-bind
reduceRegions	interaction-accessors
reduceRegions,ContactMatrix-method	ContactMatrix-accessors
reduceRegions,GInteractions-method	interaction-accessors
reduceRegions,InteractionSet-method	interaction-accessors
regions	interaction-accessors
regions,ContactMatrix-method	ContactMatrix-accessors
regions,GInteractions-method	interaction-accessors
regions,InteractionSet-method	interaction-accessors
regions<-	interaction-accessors
regions<-,ContactMatrix-method	ContactMatrix-accessors
regions<-,GInteractions-method	interaction-accessors
regions<-,InteractionSet-method	interaction-accessors
replaceRegions<-	interaction-accessors
replaceRegions<-,ContactMatrix-method	ContactMatrix-accessors
replaceRegions<-,GInteractions-method	interaction-accessors
replaceRegions<-,InteractionSet-method	interaction-accessors
resize,ContactMatrix-method	granges-methods
resize,GInteractions-method	granges-methods
resize,InteractionSet-method	granges-methods
ReverseStrictGInteractions-class	GInteractions-class
second	interaction-accessors
second,GInteractions-method	interaction-accessors
second,InteractionSet-method	interaction-accessors
seqinfo,GInteractions-method	interaction-accessors
seqinfo,InteractionSet-method	interaction-accessors
seqinfo<-,GInteractions-method	interaction-accessors
seqinfo<-,InteractionSet-method	interaction-accessors
shift,ContactMatrix-method	granges-methods
shift,GInteractions-method	granges-methods
shift,InteractionSet-method	granges-methods
show,ContactMatrix-method	ContactMatrix-accessors
show,GInteractions-method	interaction-accessors
show,InteractionSet-method	interaction-accessors
sort,ContactMatrix-method	ContactMatrix-sorting
sort,GInteractions-method	interaction-compare
sort,InteractionSet-method	interaction-compare
StrictGInteractions-class	GInteractions-class
subset,ContactMatrix-method	ContactMatrix-subset
subset,InteractionSet-method	interaction-subset
subsetByOverlaps	overlaps
subsetByOverlaps,GInteractions,GInteractions-method	overlaps
subsetByOverlaps,GInteractions,InteractionSet-method	overlaps
subsetByOverlaps,GInteractions,Vector-method	overlaps
subsetByOverlaps,InteractionSet,GInteractions-method	overlaps
subsetByOverlaps,InteractionSet,InteractionSet-method	overlaps
subsetByOverlaps,InteractionSet,Vector-method	overlaps
subsetByOverlaps,Vector,GInteractions-method	overlaps
subsetByOverlaps,Vector,InteractionSet-method	overlaps
swapAnchors	interaction-compare
swapAnchors,GInteractions-method	interaction-compare
swapAnchors,InteractionSet-method	interaction-compare
t,ContactMatrix-method	ContactMatrix-accessors
trim,ContactMatrix-method	granges-methods
trim,GInteractions-method	granges-methods
trim,InteractionSet-method	granges-methods
unique,ContactMatrix-method	ContactMatrix-sorting
unique,GInteractions-method	interaction-compare
unique,InteractionSet-method	interaction-compare
updateObject	updateObject
updateObject,GInteractions-method	updateObject
width,ContactMatrix-method	granges-methods
width,GInteractions-method	granges-methods
width,InteractionSet-method	granges-methods
[,ContactMatrix,ANY,ANY,ANY-method	ContactMatrix-subset
[,ContactMatrix,ANY,ANY-method	ContactMatrix-subset
[,ContactMatrix,ANY-method	ContactMatrix-subset
[,InteractionSet,ANY,ANY,ANY-method	interaction-subset
[,InteractionSet,ANY,ANY-method	interaction-subset
[,InteractionSet,ANY-method	interaction-subset
[<-,ContactMatrix,ANY,ANY,ContactMatrix-method	ContactMatrix-subset
[<-,GInteractions,ANY,GInteractions-method	interaction-subset
[<-,InteractionSet,ANY,ANY,InteractionSet-method	interaction-subset
