# Base Classes for Storing Genomic Interaction Data

## Documentation for package ‘InteractionSet’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D F G I L M N O P R S T U W misc

## -- A --

anchorIds<- | Interaction accessors
anchorIds<--method | ContactMatrix accessors
anchorIds<--method | Interaction accessors
anchors | Interaction accessors
anchors-method | ContactMatrix accessors
anchors-method | Interaction accessors
anchors<- | Interaction accessors
anchors<--method | ContactMatrix accessors
anchors<--method | Interaction accessors
appendRegions<- | Interaction accessors
appendRegions<--method | ContactMatrix accessors
appendRegions<--method | Interaction accessors
as.data.frame-method | Interaction accessors
as.matrix-method | ContactMatrix accessors
as.matrix<- | ContactMatrix accessors
as.matrix<--method | ContactMatrix accessors

## -- B --

boundingBox | Get the bounding box
boundingBox-method | Get the bounding box

## -- C --

c-method | Interaction subsetting and combining
cbind-method | ContactMatrix subsetting and combining
cbind-method | Interaction subsetting and combining
ContactMatrix | ContactMatrix class and constructors
ContactMatrix-access | ContactMatrix accessors
ContactMatrix-class | ContactMatrix class and constructors
ContactMatrix-dist | Compute linear distances from ContactMatrix objects
ContactMatrix-method | ContactMatrix class and constructors
ContactMatrix-sort | ContactMatrix sorting and ordering
ContactMatrix-subset | ContactMatrix subsetting and combining
countOverlaps | Find overlaps between interactions in one or two dimensions
countOverlaps-method | Find overlaps between interactions in one or two dimensions

## -- D --

deflate | Convert between classes
deflate-method | Convert between classes
dim-method | ContactMatrix accessors
dimnames-method | ContactMatrix accessors
dimnames<--method | ContactMatrix accessors
duplicated-method | ContactMatrix sorting and ordering
duplicated-method | Interaction comparisons

## -- F --

findOverlaps | Find overlaps between interactions in one or two dimensions
findOverlaps-method | Find overlaps between interactions in one or two dimensions
first | Interaction accessors
first-method | Interaction accessors

## -- G --

GInteractions | GInteractions class and constructors
GInteractions-class | GInteractions class and constructors
GInteractions-method | GInteractions class and constructors

## -- I --

inflate | Convert between classes
inflate-method | Convert between classes
interaction-access | Interaction accessors
interaction-compare | Interaction comparisons
Interaction-overlaps | Find overlaps between interactions in one or two dimensions
interaction-subset | Interaction subsetting and combining
interactions | Interaction accessors
interactions-method | Interaction accessors
interactions<- | Interaction accessors
interactions<--method | Interaction accessors
InteractionSet | InteractionSet class and constructors
InteractionSet-class | InteractionSet class and constructors
InteractionSet-method | InteractionSet class and constructors
intrachr | Get the linear distance for each interaction
intrachr-method | Compute linear distances from ContactMatrix objects
intrachr-method | Get the linear distance for each interaction

## -- L --

length-method | ContactMatrix accessors
length-method | Interaction accessors
linearize | Linearize 2D interactions into 1D ranges
linearize-method | Linearize 2D interactions into 1D ranges
linkOverlaps | Link overlapping regions
linkOverlaps-method | Link overlapping regions

## -- M --

makeGInteractionsFromGRangesPairs | Extract paired ranges
match-method | Interaction comparisons
mcols-method | Interaction accessors
mcols<--method | Interaction accessors

## -- N --

names-method | Interaction accessors
names<--method | Interaction accessors

## -- O --

order-method | ContactMatrix sorting and ordering
order-method | Interaction comparisons
overlapsAny | Find overlaps between interactions in one or two dimensions
overlapsAny-method | Find overlaps between GRanges and a ContactMatrix
overlapsAny-method | Find overlaps between interactions in one or two dimensions

## -- P --

pairdist | Get the linear distance for each interaction
pairdist-method | Compute linear distances from ContactMatrix objects
pairdist-method | Get the linear distance for each interaction
pairs | Extract paired ranges
pairs-method | Extract paired ranges
pcompare-method | Interaction comparisons

## -- R --

rbind-method | ContactMatrix subsetting and combining
rbind-method | Interaction subsetting and combining
reduceRegions | Interaction accessors
reduceRegions-method | ContactMatrix accessors
reduceRegions-method | Interaction accessors
regions | Interaction accessors
regions-method | ContactMatrix accessors
regions-method | Interaction accessors
regions<- | Interaction accessors
regions<--method | ContactMatrix accessors
regions<--method | Interaction accessors
replaceRegions<- | Interaction accessors
replaceRegions<--method | ContactMatrix accessors
replaceRegions<--method | Interaction accessors
ReverseStrictGInteractions-class | GInteractions class and constructors

## -- S --

second | Interaction accessors
second-method | Interaction accessors
seqinfo-method | Interaction accessors
seqinfo<--method | Interaction accessors
show-method | ContactMatrix accessors
show-method | Interaction accessors
sort-method | ContactMatrix sorting and ordering
sort-method | Interaction comparisons
split-method | Interaction subsetting and combining
StrictGInteractions-class | GInteractions class and constructors
subset-method | ContactMatrix subsetting and combining
subset-method | Interaction subsetting and combining
subsetByOverlaps | Find overlaps between interactions in one or two dimensions
subsetByOverlaps-method | Find overlaps between interactions in one or two dimensions
swapAnchors | Interaction comparisons
swapAnchors-method | Interaction comparisons

## -- T --

t-method | ContactMatrix accessors
trim-method | Equivalents of GRanges methods

## -- U --

unique-method | ContactMatrix sorting and ordering
unique-method | Interaction comparisons

## -- W --

width-method | Equivalents of GRanges methods

## -- misc --

$-method | Interaction accessors
$<--method | Interaction accessors
[-method | ContactMatrix subsetting and combining
[-method | Interaction subsetting and combining
[<--method | ContactMatrix subsetting and combining
[<--method | Interaction subsetting and combining