# Utilities for handling genomic interaction data

## Documentation for package ‘GenomicInteractions’ version 1.40.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

GenomicInteractions-package | GenomicInteractions
.importHicLib | Function to read in processed Hi-C interaction data generated by hiclib
.importHomer | Function to read in processed Hi-C interaction data generated by HOMER
.processChiapetName | Function to process names relating to interactions stored in bed12 formats.
.readBam | Function to read in interaction-data stored in a BAM file
.readTwoBams | Function to read in interaction-data stored in a pair of BAM files
.validateInput | Function to validate tabular input
anchorOne | Functions to access data held in a GenomicInteractions object.
anchorOne-method | Functions to access data held in a GenomicInteractions object.
anchorTwo | Functions to access data held in a GenomicInteractions object.
anchorTwo-method | Functions to access data held in a GenomicInteractions object.
annotateInteractions | Annotate the interactions in a GInteractions object
annotateInteractions-method | Annotate the interactions in a GInteractions object
annotateRegions | Annotate regions
annotateRegions-method | Annotate regions
annotationFeatures | Functions to access data held in a GenomicInteractions object.
annotationFeatures-method | Functions to access data held in a GenomicInteractions object.
asBED-method | Coerce to BED structure
availableDisplayPars | The default display parameters for a track object class can be queries using the availableDisplayPars function.
calculateDistances | Calculate interaction distances
calculateDistances-method | Calculate interaction distances
categoriseInteractions | Get the numbers of interaction types existing in your data
chromosome-method | A class to hold chromatin interaction data for a specific genomic region
countsBetweenAnchors | Summarise interactions between defined anchors
countsBetweenAnchors-method | Summarise interactions between defined anchors
description-method | Functions to access data held in a GenomicInteractions object.
description<--method | Functions to set data held in a GInteractions object.
end-method | A class to hold chromatin interaction data for a specific genomic region
export.bed12 | Export interactions in BED12 format.
export.bed12-method | Export interactions in BED12 format.
export.bedpe | Export interactions in BED Paired-End format.
export.bedpe-method | Export interactions in BED Paired-End format.
export.chiasig | Export interactions in a BEDPE-like format for use with ChiaSig
export.chiasig-method | Export interactions in a BEDPE-like format for use with ChiaSig
export.igraph | Export interactions to an igraph object.
export.igraph-method | Export interactions to an igraph object.
GenomicInteractions | Function to create a GenomicInteractions object
GenomicInteractions-class | A S4 class to represent interactions between genomic regions.
GenomicInteractions-method | Function to create a GenomicInteractions object
getters | Functions to access data held in a GenomicInteractions object.
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
hg19.refseq.transcripts | Human Refseq transcripts from chr 17-18
hic_example_data | Example HiC dataset
interactionCounts | Functions to access data held in a GenomicInteractions object.
interactionCounts-method | Functions to access data held in a GenomicInteractions object.
interactionCounts<- | Functions to set data held in a GInteractions object.
interactionCounts<--method | Functions to set data held in a GInteractions object.
InteractionHelpers | Interaction Type Helpers
InteractionTrack | Constructor to create an InteractionTrack object
InteractionTrack-class | A class to hold chromatin interaction data for a specific genomic region
is.cis | Interaction Type Helpers
is.cis-method | Interaction Type Helpers
is.dd | Interaction Type Helpers
is.dd-method | Interaction Type Helpers
is.dt | Interaction Type Helpers
is.dt-method | Interaction Type Helpers
is.pd | Interaction Type Helpers
is.pd-method | Interaction Type Helpers
is.pp | Interaction Type Helpers
is.pp-method | Interaction Type Helpers
is.pt | Interaction Type Helpers
is.pt-method | Interaction Type Helpers
is.trans | Interaction Type Helpers
is.trans-method | Interaction Type Helpers
is.tt | Interaction Type Helpers
is.tt-method | Interaction Type Helpers
isInteractionType | Interaction Type Helpers
isInteractionType-method | Interaction Type Helpers
makeGenomicInteractionsFromFile | Function to create GenomicInteraction objects from a file
mm9_refseq_promoters | Mouse Refseq promoters from chr 14-15
name | Functions to access data held in a GenomicInteractions object.
name-method | Functions to access data held in a GenomicInteractions object.
name<- | Functions to set data held in a GInteractions object.
name<--method | Functions to set data held in a GInteractions object.
plotAvgViewpoint | Plot coverage around a set of virtual 4C viewpoints
plotCisTrans | Plots the percentages of cis and trans interactions for a GInteractions object as a donut plot.
plotCounts | Plot a bar chart of the number of interactions supported by different numbers of reads in your data.
plotDists | Plots a histogram of interaction distances for a GInteractions Object
plotInteractionAnnotations | Plot a donut plot of interaction types for an annotated GInteractions object
plotSummaryStats | Plot summary statistics for a GInteractions object
plotViewpoint | Plot coverage around a virtual 4C viewpoint
removeDups | Remove all but one occurences of a duplicated interaction
resetAnnotations | Reset annotations made to a GInteractions object
resetAnnotations-method | Reset annotations made to a GInteractions object
sameStrand | Tests whether anchors have the same strand.
setters | Functions to set data held in a GInteractions object.
start-method | A class to hold chromatin interaction data for a specific genomic region
subset-method | A class to hold chromatin interaction data for a specific genomic region
subsetByFeatures | Subset a GInteractions object by features
subsetByFeatures-method | Subset a GInteractions object by features
sum-method | Return the total number of interactions in a GInteractions GIObject
summariseByFeaturePairs | Summarise the number of interactions between two sets of features.
summariseByFeaturePairs-method | Summarise the number of interactions between two sets of features.
summariseByFeatures | Summary statistics of interactions for a given feature set
summariseByFeatures-method | Summary statistics of interactions for a given feature set
thymus_enh | Putative enhancers from mouse thymus data
updateObject-method | updateObject method for GenomicInteractions 1.3.7 and earlier
viewPoint | Virtual 4C viewpoint