InteractionSet: Base Classes for Storing Genomic Interaction Data

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>
Date of publicationNone
MaintainerAaron Lun <alun@wehi.edu.au>
LicenseGPL-3
Version1.2.1

View on Bioconductor

Functions

anchors Man page
anchors<- Man page
anchors<-,ContactMatrix-method Man page
anchors,ContactMatrix-method Man page
anchors<-,GInteractions-method Man page
anchors,GInteractions-method Man page
anchors<-,InteractionSet-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<- Man page
as.matrix<-,ContactMatrix-method Man page
as.matrix,ContactMatrix-method Man page
boundingBox Man page
boundingBox,GInteractions-method Man page
boundingBox,InteractionSet-method Man page
cbind,ContactMatrix-method Man page
cbind,InteractionSet-method Man page
c,GInteractions-method Man page
c,InteractionSet-method Man page
ContactMatrix Man page
ContactMatrix-access Man page
[,ContactMatrix,ANY,ANY,ANY-method Man page
[<-,ContactMatrix,ANY,ANY,ContactMatrix-method Man page
[,ContactMatrix,ANY,ANY-method Man page
ContactMatrix,ANY,GRanges,GRanges,GenomicRangesORmissing-method Man page
[,ContactMatrix,ANY-method Man page
ContactMatrix,ANY,numeric,numeric,GRanges-method Man page
ContactMatrix-class Man page
ContactMatrix-dist Man page
ContactMatrix,missing,missing,missing,GenomicRangesORmissing-met Man page
ContactMatrix-sort Man page
ContactMatrix-subset Man page
countOverlaps Man page
countOverlaps,GInteractions,GInteractions-method Man page
countOverlaps,GInteractions,InteractionSet-method Man page
countOverlaps,GInteractions,missing-method Man page
countOverlaps,GInteractions,Vector-method Man page
countOverlaps,InteractionSet,GInteractions-method Man page
countOverlaps,InteractionSet,InteractionSet-method Man page
countOverlaps,InteractionSet,missing-method Man page
countOverlaps,InteractionSet,Vector-method Man page
countOverlaps,Vector,GInteractions-method Man page
countOverlaps,Vector,InteractionSet-method Man page
deflate Man page
deflate,ContactMatrix-method Man page
dim,ContactMatrix-method Man page
dimnames<-,ContactMatrix,ANY-method Man page
dimnames<-,ContactMatrix-method Man page
dimnames,ContactMatrix-method Man page
duplicated,ContactMatrix-method Man page
duplicated,GInteractions-method Man page
duplicated,InteractionSet-method Man page
findOverlaps Man page
findOverlaps,GInteractions,GInteractions-method Man page
findOverlaps,GInteractions,InteractionSet-method Man page
findOverlaps,GInteractions,missing-method Man page
findOverlaps,GInteractions,Vector-method Man page
findOverlaps,InteractionSet,GInteractions-method Man page
findOverlaps,InteractionSet,InteractionSet-method Man page
findOverlaps,InteractionSet,missing-method Man page
findOverlaps,InteractionSet,Vector-method Man page
findOverlaps,Vector,GInteractions-method Man page
findOverlaps,Vector,InteractionSet-method Man page
GInteractions Man page
[<-,GInteractions,ANY,ANY,GInteractions-method Man page
[,GInteractions,ANY,ANY-method Man page
[,GInteractions,ANY-method Man page
GInteractions-class Man page
GInteractions,GRanges,GRanges,GenomicRangesORmissing-method Man page
$<-,GInteractions-method Man page
$,GInteractions-method Man page
GInteractions,missing,missing,GenomicRangesORmissing-method Man page
GInteractions,numeric,numeric,GRanges-method Man page
inflate Man page
inflate,GInteractions-method Man page
inflate,InteractionSet-method Man page
interaction-access Man page
interaction-compare Man page
Interaction-overlaps Man page
interactions Man page
interactions<- Man page
InteractionSet Man page
[,InteractionSet,ANY,ANY,ANY-method Man page
[<-,InteractionSet,ANY,ANY,InteractionSet-method Man page
[,InteractionSet,ANY,ANY-method Man page
InteractionSet,ANY,GInteractions-method Man page
[,InteractionSet,ANY-method Man page
InteractionSet-class Man page
InteractionSet,missing,missing-method Man page
interactions<-,InteractionSet-method Man page
interactions,InteractionSet-method Man page
interaction-subset 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
linearize Man page
linearize,GInteractions,GRanges-method Man page
linearize,GInteractions,numeric-method Man page
linearize,InteractionSet,GRanges-method Man page
linearize,InteractionSet,numeric-method Man page
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
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,GInteractions-method Man page
names<-,InteractionSet-method Man page
names,InteractionSet-method Man page
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,GRangesList-method Man page
overlapsAny,ContactMatrix,GRanges-method Man page
overlapsAny,ContactMatrix,InteractionSet-method Man page
overlapsAny,GInteractions,GInteractions-method Man page
overlapsAny,GInteractions,InteractionSet-method Man page
overlapsAny,GInteractions,missing-method Man page
overlapsAny,GInteractions,Vector-method Man page
overlapsAny,InteractionSet,GInteractions-method Man page
overlapsAny,InteractionSet,InteractionSet-method Man page
overlapsAny,InteractionSet,missing-method Man page
overlapsAny,InteractionSet,Vector-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
pairs Man page
pairs,GInteractions-method Man page
pairs,InteractionSet-method Man page
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<- Man page
regions<-,ContactMatrix-method Man page
regions,ContactMatrix-method Man page
regions<-,GInteractions-method Man page
regions,GInteractions-method Man page
regions<-,InteractionSet-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
ReverseStrictGInteractions-class Man page
seqinfo<-,GInteractions-method Man page
seqinfo,GInteractions-method Man page
seqinfo<-,InteractionSet-method Man page
seqinfo,InteractionSet-method Man page
show,ContactMatrix-method Man page
show,GInteractions-method Man page
show,InteractionSet-method Man page
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
StrictGInteractions-class 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
subset,ContactMatrix-method Man page
subset,GInteractions-method Man page
subset,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
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

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.