InteractionSet: Base Classes for Storing Genomic Interaction Data
Version 1.4.0

Provides the GInteractions, InteractionSet and ContactMatrix objects and associated methods for storing and manipulating genomic interaction data from Hi-C and ChIA-PET experiments.

AuthorAaron Lun <alun@wehi.edu.au>, Malcolm Perry <mgperry32@gmail.com>, Liz Ing-Simmons <liz.ing-simmons12@csc.mrc.ac.uk>
Bioconductor views DataRepresentation HiC Infrastructure Software
Date of publicationNone
MaintainerAaron Lun <alun@wehi.edu.au>
LicenseGPL-3
Version1.4.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("InteractionSet")

Popular man pages

ContactMatrix-sorting: ContactMatrix sorting and ordering
GInteractions-class: GInteractions class and constructors
granges-methods: Equivalents of GRanges methods
interaction-accessors: Interaction accessors
interaction-subset: Interaction subsetting and combining
linkOverlaps: Link overlapping regions
pairs: Extract paired ranges
See all...

All man pages Function index File listing

Man pages

boundingBox: Get the bounding box
ContactMatrix-accessors: ContactMatrix accessors
ContactMatrix-class: ContactMatrix class and constructors
ContactMatrix-distances: Compute linear distances from ContactMatrix objects
ContactMatrix-overlaps: Find overlaps between GRanges and a ContactMatrix
ContactMatrix-sorting: ContactMatrix sorting and ordering
ContactMatrix-subset: ContactMatrix subsetting and combining
conversion: Convert between classes
distances: Get the linear distance for each interaction
GInteractions-class: GInteractions class and constructors
granges-methods: Equivalents of GRanges methods
interaction-accessors: Interaction accessors
interaction-compare: Interaction comparisons
InteractionSet-class: InteractionSet class and constructors
interaction-subset: Interaction subsetting and combining
linearize: Linearize 2D interactions into 1D ranges
linkOverlaps: Link overlapping regions
overlaps: Find overlaps between interactions in one or two dimensions
pairs: Extract paired ranges

Functions

$,GInteractions-method Man page
$<-,GInteractions-method Man page
ContactMatrix Man page
ContactMatrix,ANY,GRanges,GRanges,GenomicRangesORmissing-method Man page
ContactMatrix,ANY,numeric,numeric,GRanges-method Man page
ContactMatrix,missing,missing,missing,GenomicRangesORmissing-met Man page
ContactMatrix-access Man page
ContactMatrix-class Man page
ContactMatrix-dist Man page
ContactMatrix-sort Man page
ContactMatrix-subset Man page
GInteractions Man page
GInteractions,GRanges,GRanges,GenomicRangesORmissing-method Man page
GInteractions,missing,missing,GenomicRangesORmissing-method Man page
GInteractions,numeric,numeric,GRanges-method Man page
GInteractions-class Man page
ISetToRSE Source code
Interaction-overlaps Man page
InteractionSet Man page
InteractionSet,ANY,GInteractions-method Man page
InteractionSet,missing,missing-method Man page
InteractionSet-class Man page
ReverseStrictGInteractions-class Man page
StrictGInteractions-class Man page
[,ContactMatrix,ANY,ANY,ANY-method Man page
[,ContactMatrix,ANY,ANY-method Man page
[,ContactMatrix,ANY-method Man page
[,GInteractions,ANY,ANY-method Man page
[,GInteractions,ANY-method Man page
[,InteractionSet,ANY,ANY,ANY-method Man page
[,InteractionSet,ANY,ANY-method Man page
[,InteractionSet,ANY-method Man page
[<-,ContactMatrix,ANY,ANY,ContactMatrix-method Man page
[<-,GInteractions,ANY,ANY,GInteractions-method Man page
[<-,InteractionSet,ANY,ANY,InteractionSet-method Man page
anchor.fun.gen Source code
anchor.repfun.gen Source code
anchorIds<- Man page
anchorIds<-,ContactMatrix-method Man page
anchorIds<-,GInteractions-method Man page
anchorIds<-,InteractionSet-method Man page
anchorIds<-,ReverseStrictGInteractions-method Man page
anchorIds<-,StrictGInteractions-method Man page
anchors Man page
anchors,ContactMatrix-method Man page
anchors,GInteractions-method Man page
anchors,InteractionSet-method Man page
anchors<- Man page
anchors<-,ContactMatrix-method Man page
anchors<-,GInteractions-method Man page
anchors<-,InteractionSet-method Man page
anchors<-,ReverseStrictGInteractions-method Man page
anchors<-,StrictGInteractions-method Man page
appendRegions<- Man page
appendRegions<-,ContactMatrix-method Man page
appendRegions<-,GInteractions-method Man page
appendRegions<-,InteractionSet-method Man page
as.data.frame,GInteractions-method Man page
as.matrix,ContactMatrix-method Man page
as.matrix<- Man page
as.matrix<-,ContactMatrix-method Man page
boundingBox Man page Source code
boundingBox,GInteractions-method Man page
boundingBox,InteractionSet-method Man page
c,GInteractions-method Man page
c,InteractionSet-method Man page
cbind,ContactMatrix-method Man page
cbind,InteractionSet-method Man page
check_inputs Source code
chooseRegion Source code
coerce_to_union Source code
collate_GRanges Source code
countOverlaps Man page
countOverlaps,GInteractions,GInteractions-method Man page
countOverlaps,GInteractions,InteractionSet-method Man page
countOverlaps,GInteractions,Vector-method Man page
countOverlaps,GInteractions,missing-method Man page
countOverlaps,InteractionSet,GInteractions-method Man page
countOverlaps,InteractionSet,InteractionSet-method Man page
countOverlaps,InteractionSet,Vector-method Man page
countOverlaps,InteractionSet,missing-method Man page
countOverlaps,Vector,GInteractions-method Man page
countOverlaps,Vector,InteractionSet-method Man page
decode_region_mode Source code
deflate Man page
deflate,ContactMatrix-method Man page
dim,ContactMatrix-method Man page
dimnames,ContactMatrix-method Man page
dimnames<-,ContactMatrix,ANY-method Man page
dimnames<-,ContactMatrix-method Man page
duplicated,ContactMatrix-method Man page
duplicated,GInteractions-method Man page
duplicated,InteractionSet-method Man page
enforce_order Source code
fast_overlap Source code
findOverlaps Man page
findOverlaps,GInteractions,GInteractions-method Man page
findOverlaps,GInteractions,InteractionSet-method Man page
findOverlaps,GInteractions,Vector-method Man page
findOverlaps,GInteractions,missing-method Man page
findOverlaps,InteractionSet,GInteractions-method Man page
findOverlaps,InteractionSet,InteractionSet-method Man page
findOverlaps,InteractionSet,Vector-method Man page
findOverlaps,InteractionSet,missing-method Man page
findOverlaps,Vector,GInteractions-method Man page
findOverlaps,Vector,InteractionSet-method Man page
first Man page
first,GInteractions-method Man page
first,InteractionSet-method Man page
flipGI Source code
get_dist_output Source code
get_olap_bounds Source code
get_used Source code
inflate Man page
inflate,GInteractions-method Man page
inflate,InteractionSet-method Man page
interaction-access Man page
interaction-compare Man page
interaction-subset Man page
interactions Man page
interactions,InteractionSet-method Man page
interactions<- Man page
interactions<-,InteractionSet-method Man page
intrachr Man page
intrachr,ContactMatrix-method Man page
intrachr,GInteractions-method Man page
intrachr,InteractionSet-method Man page
length,ContactMatrix-method Man page
length,GInteractions-method Man page
linear_olap_finder Source code
linearize Man page Source code
linearize,GInteractions,GRanges-method Man page
linearize,GInteractions,numeric-method Man page
linearize,InteractionSet,GRanges-method Man page
linearize,InteractionSet,numeric-method Man page
linkOverlap Source code
linkOverlaps Man page
linkOverlaps,GInteractions,GRanges,GRanges-method Man page
linkOverlaps,GInteractions,GRanges,missing-method Man page
linkOverlaps,InteractionSet,GRanges,GRanges-method Man page
linkOverlaps,InteractionSet,GRanges,missing-method Man page
makeGInteractionsFromGRangesPairs Man page Source code
makeNakedMatFromGInteractions Source code
make_to_indices Source code
match,GInteractions,GInteractions-method Man page
match,GInteractions,InteractionSet-method Man page
match,InteractionSet,GInteractions-method Man page
match,InteractionSet,InteractionSet-method Man page
mcols,InteractionSet-method Man page
mcols<-,InteractionSet-method Man page
names,GInteractions-method Man page
names,InteractionSet-method Man page
names<-,GInteractions-method Man page
names<-,InteractionSet-method Man page
new_ContactMatrix Source code
new_GInteractions Source code
new_InteractionSet Source code
olap.fun.gen Source code
order,ContactMatrix-method Man page
order,GInteractions-method Man page
order,InteractionSet-method Man page
overlapsAny Man page
overlapsAny,ContactMatrix,GInteractions-method Man page
overlapsAny,ContactMatrix,GRanges-method Man page
overlapsAny,ContactMatrix,GRangesList-method Man page
overlapsAny,ContactMatrix,InteractionSet-method Man page
overlapsAny,GInteractions,GInteractions-method Man page
overlapsAny,GInteractions,InteractionSet-method Man page
overlapsAny,GInteractions,Vector-method Man page
overlapsAny,GInteractions,missing-method Man page
overlapsAny,InteractionSet,GInteractions-method Man page
overlapsAny,InteractionSet,InteractionSet-method Man page
overlapsAny,InteractionSet,Vector-method Man page
overlapsAny,InteractionSet,missing-method Man page
overlapsAny,Vector,GInteractions-method Man page
overlapsAny,Vector,InteractionSet-method Man page
pairdist Man page
pairdist,ContactMatrix-method Man page
pairdist,GInteractions-method Man page
pairdist,InteractionSet-method Man page
paired_overlap_finder2 Source code
pairs Man page
pairs,GInteractions-method Man page
pairs,InteractionSet-method Man page
pasteAnchor Source code
pcompare,GInteractions,GInteractions-method Man page
rbind,ContactMatrix-method Man page
rbind,GInteractions-method Man page
rbind,InteractionSet-method Man page
reduceRegions Man page
reduceRegions,ContactMatrix-method Man page
reduceRegions,GInteractions-method Man page
reduceRegions,InteractionSet-method Man page
regions Man page
regions,ContactMatrix-method Man page
regions,GInteractions-method Man page
regions,InteractionSet-method Man page
regions<- Man page
regions<-,ContactMatrix-method Man page
regions<-,GInteractions-method Man page
regions<-,InteractionSet-method Man page
replaceRegions<- Man page
replaceRegions<-,ContactMatrix-method Man page
replaceRegions<-,GInteractions-method Man page
replaceRegions<-,InteractionSet-method Man page
resort_regions Source code
safeNMcols Source code
scat Source code
second Man page
second,GInteractions-method Man page
second,InteractionSet-method Man page
seqinfo,GInteractions-method Man page
seqinfo,InteractionSet-method Man page
seqinfo<-,GInteractions-method Man page
seqinfo<-,InteractionSet-method Man page
show,ContactMatrix-method Man page
show,GInteractions-method Man page
show,InteractionSet-method Man page
showGInteractions Source code
sort,ContactMatrix-method Man page
sort,GInteractions-method Man page
sort,InteractionSet-method Man page
split,GInteractions-method Man page
split,InteractionSet-method Man page
strict_check Source code
subset,ContactMatrix-method Man page
subset,GInteractions-method Man page
subset,InteractionSet-method Man page
subsetByOverlaps Man page
subsetByOverlaps,GInteractions,GInteractions-method Man page
subsetByOverlaps,GInteractions,InteractionSet-method Man page
subsetByOverlaps,GInteractions,Vector-method Man page
subsetByOverlaps,InteractionSet,GInteractions-method Man page
subsetByOverlaps,InteractionSet,InteractionSet-method Man page
subsetByOverlaps,InteractionSet,Vector-method Man page
subsetByOverlaps,Vector,GInteractions-method Man page
subsetByOverlaps,Vector,InteractionSet-method Man page
swapAnchors Man page
swapAnchors,GInteractions-method Man page
swapAnchors,InteractionSet-method Man page
t,ContactMatrix-method Man page
trim,ContactMatrix-method Man page
trim,GInteractions-method Man page
trim,InteractionSet-method Man page
unflipGI Source code
unique,ContactMatrix-method Man page
unique,GInteractions-method Man page
unique,InteractionSet-method Man page
width,ContactMatrix-method Man page
width,GInteractions-method Man page
width,InteractionSet-method Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/ContactMatrix-methods.R
R/GInteractions-methods.R
R/GRanges-methods.R
R/InteractionSet-methods.R
R/boundingBox.R
R/conversion.R
R/distances.R
R/getset.R
R/linearize.R
R/linkOverlaps.R
R/matching.R
R/overlaps.R
R/pairs.R
R/swapAnchors.R
build
build/vignette.rds
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/interactions.R
inst/doc/interactions.Rmd
inst/doc/interactions.html
man
man/ContactMatrix-accessors.Rd
man/ContactMatrix-class.Rd
man/ContactMatrix-distances.Rd
man/ContactMatrix-overlaps.Rd
man/ContactMatrix-sorting.Rd
man/ContactMatrix-subset.Rd
man/GInteractions-class.Rd
man/InteractionSet-class.Rd
man/boundingBox.Rd
man/conversion.Rd
man/distances.Rd
man/granges-methods.Rd
man/interaction-accessors.Rd
man/interaction-compare.Rd
man/interaction-subset.Rd
man/linearize.Rd
man/linkOverlaps.Rd
man/overlaps.Rd
man/pairs.Rd
src
src/box_bounds.cpp
src/init.cpp
src/iset.h
src/overlaps.cpp
tests
tests/testthat
tests/testthat.R
tests/testthat/test-CM.R
tests/testthat/test-GI.R
tests/testthat/test-IS.R
tests/testthat/test-box.R
tests/testthat/test-compare.R
tests/testthat/test-convert.R
tests/testthat/test-dist.R
tests/testthat/test-grmeth.R
tests/testthat/test-linear.R
tests/testthat/test-link.R
tests/testthat/test-olap.R
vignettes
vignettes/interactions.Rmd
InteractionSet documentation built on May 20, 2017, 10:54 p.m.

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