GenomicInteractions v1.6.2

by Malcolm Perry

R package for handling genomic interaction data

R package for handling Genomic interaction data, such as ChIA-PET/Hi-C, annotating genomic features with interaction information and producing various plots / statistics.

Readme

##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.

Functions in GenomicInteractions

Name Description
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
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