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##GenomicInteractions

GenomicInteractions is an R/Bioconductor package for manipulating and investigating chromatin interaction data. It provides simple annotation of genomic features which interfaces with existing Bioconductor packages, as well as numerous plotting functions and summary statistics.

###Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("GenomicInteractions")

To install the latest version from this repository using the devtools package:

library(devtools)
install_github("ComputationalRegulatoryGenomicsICL/GenomicInteractions")

###Bioconductor links and documentation

The bioconductor page contains documentation for the released package: Bioconductior Release 3.0

To view example Hi-C and ChIA-PET analysis for using this package on your system, start R and enter:

browseVignettes("GenomicInteractions")

###Citation

From within R, enter citation("GenomicInteractions"):

Harmston, N., Ing-Simmons, E., Perry, M., Baresic, A., and Lenhard, B. (2014). GenomicInteractions: R package for handling genomic interaction data. R package version 1.0.0.

###Contributing

We welcome contributions in any form: suggestions, issues, bugfixes. Pull requests should be made to the development branch.

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Version

Version

1.6.2

License

GPL-3

Issues

8

Pull Requests

0

Stars

7

Forks

0

Maintainer

Malcolm Perry

Last Published

February 15th, 2017

Functions in GenomicInteractions (1.6.2)

export.bed12

Export interactions in BED12 format.
export.igraph

Export interactions to an igraph object.
GenomicInteractions-package

A package for looking at genomic interaction data.
thymus_enh

Putative enhancers from mouse thymus data
get_binom_ligation_threshold

get self ligation threshold with binomial test
get_self_ligation_threshold

Get self ligation threshold with SD method from Heidari et al
sum,GInteractions-method

Return the total number of interactions in a GInteractions GIObject
availableDisplayPars

The default display parameters for a track object class can be queries using the availableDisplayPars function.
asBED,GInteractions-method

Coerce to BED structure
hg19.refseq.transcripts

Human Refseq transcripts from chr 17-18
calculateDistances

Calculate interaction distances
subsetByFeatures

Subset a GInteractions object by features
export.bedpe

Export interactions in BED Paired-End format.
InteractionTrack-class

A class to hold chromatin interaction data for a specific genomic region.
plotInteractionAnnotations

Plot a donut plot of interaction types for an annotated GInteractions object
annotateInteractions

Annotate the interactions in a GInteractions object
countsBetweenAnchors

Summarise interactions between defined anchors
sameStrand

Tests whether anchors have the same strand.
summariseByFeaturePairs

Summarise the number of interactions between two sets of features.
mm9_refseq_promoters

Mouse Refseq promoters from chr 14-15
plotDists

Plots a histogram of interaction distances for a GInteractions Object
viewPoint

Virtual 4C viewpoint
updateObject,GenomicInteractions-method

updateObject method for GenomicInteractions 1.3.7 and earlier
annotateAnchors

Annotate anchors - DEPRECATED
plotViewpoint

Plot coverage around a virtual 4C viewpoint
removeDups

Remove all but one occurences of a duplicated interaction
is.pp

Interaction Type Helpers
annotateRegions

Annotate regions
categoriseInteractions

Get the numbers of interaction types existing in your data
export.chiasig

Export interactions in a BEDPE-like format for use with ChiaSig
getters

Functions to access data held in a GenomicInteractions object.
resetAnnotations

Reset annotations made to a GInteractions object
GenomicInteractions-class

A S4 class to represent interactions between genomic regions.
plotCisTrans

Plots the percentages of cis and trans interactions for a GInteractions object as a donut plot.
makeGenomicInteractionsFromFile

Function to create GenomicInteraction objects from a file
summariseByFeatures

Summary statistics of interactions for a given feature set
setters

Functions to set data held in a GInteractions object.
plotAvgViewpoint

Plot coverage around a set of virtual 4C viewpoints
GenomicInteractions

Function to create a GenomicInteractions object
InteractionTrack

Constructor to create an InteractionTrack object
hic_example_data

Example HiC dataset
plotCounts

Plot a bar chart of the number of interactions supported by different numbers of reads in your data.
plotSummaryStats

Plot summary statistics for a GInteractions object