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.

Author
Aaron Lun <alun@wehi.edu.au>, Malcolm Perry <mgperry32@gmail.com>, Liz Ing-Simmons <liz.ing-simmons12@csc.mrc.ac.uk>
Date of publication
None
Maintainer
Aaron Lun <alun@wehi.edu.au>
License
GPL-3
Version
1.2.0

View on Bioconductor

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

Files in this package

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