Base Classes for Storing Genomic Interaction Data

Documentation for package ‘InteractionSet’ version 1.30.0

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-- A --

-- B --

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

-- C --

c-method	Interaction combining
cbind-method	ContactMatrix subsetting and combining
cbind-method	Interaction 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
flank-method	Equivalents of GRanges methods

-- 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-bind	Interaction combining
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
narrow-method	Equivalents of GRanges methods

-- 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 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
resize-method	Equivalents of GRanges methods
ReverseStrictGInteractions-class	GInteractions class and constructors

-- S --

second	Interaction accessors
second-method	Interaction accessors
seqinfo-method	Interaction accessors
seqinfo<--method	Interaction accessors
shift-method	Equivalents of GRanges methods
show-method	ContactMatrix accessors
show-method	Interaction accessors
sort-method	ContactMatrix sorting and ordering
sort-method	Interaction comparisons
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
updateObject	Update a GInteractions object
updateObject-method	Update a GInteractions object

-- W --

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