Base Classes for Storing Genomic Interaction Data


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Documentation for package ‘InteractionSet’ version 1.12.0

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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
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 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

-- 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