# R package for handling genomic interaction data

## Documentation for package ‘GenomicInteractions’ version 1.2.3

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

## Help Pages

GenomicInteractions-package | A package for looking at genomic interaction data.
$-method | Quick access to GenomicInteractions metadata columns
$<--method | Quick access to GenomicInteractions metadata columns
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.
annotateAnchors | Annotate anchors
annotateAnchors-method | Annotate anchors
annotateInteractions | Annotate the interactions in a GenomicInteractions object
annotateInteractions-method | Annotate the interactions in a GenomicInteractions object
annotationFeatures | Functions to access data held in a GenomicInteractions object.
annotationFeatures-method | Functions to access data held in a GenomicInteractions object.
c | Combine GenomicInteractions Methods
c-method | Combine GenomicInteractions Methods
calculateDistances | Calculate interaction distances
calculateDistances-method | Calculate interaction distances
capitalize | Capitalize first letter of string
categoriseInteractions | Get the numbers of interaction types existing in your data
countOverlaps-method | Find overlaps between GRanges and GenomicInteractions objects
countsBetweenAnchors | Summarise Interactions between defined anchors
countsBetweenAnchors-method | Summarise Interactions between defined anchors
description | Functions to access data held in a GenomicInteractions object.
description-method | Functions to access data held in a GenomicInteractions object.
description<- | Functions to set data held in a GenomicInteractions object.
description<--method | Functions to set data held in a GenomicInteractions object.
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.
findOverlaps | Find overlaps between GRanges and GenomicInteractions objects
findOverlaps-method | Find overlaps between GRanges and GenomicInteractions objects
GenomicInteractions | Function to create a GenomicInteraction object
GenomicInteractions-class | A S4 class to represent interactions between genomic regions.
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 GenomicInteractions object.
interactionCounts<--method | Functions to set data held in a GenomicInteractions object.
InteractionHelpers | Interaction Type Helpers
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
length-method | Get the length of a GenomicInteractions GIObject
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 GenomicInteractions object.
name<--method | Functions to set data held in a GenomicInteractions object.
overlapsAny-method | Find overlaps between GRanges and GenomicInteractions objects
plotCisTrans | Plots the percentages of cis and trans interactions for a GenomicInteractions 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 GenomicInteractions Object
plotInteractionAnnotations | Plot a donut plot of interaction types for an annotated GenomicInteractions object
plotSummaryStats | Plot summary statistics for a GenomicInteractions object
plotViewpoint | Plot coverage around a virtual 4C viewpoint
print-method | Print function for GenomicInteractions
removeDups | Remove all but one occurences of a duplicated interaction
resetAnnotations | Reset annotations made to a GenomicInteractions object
resetAnnotations-method | Reset annotations made to a GenomicInteractions object
sameStrand | Tests whether anchors have the same strand.
seqinfo-method | Acessing/modifying sequence information for a GenomicInteractions object
seqinfo<--method | Acessing/modifying sequence information for a GenomicInteractions object
setters | Functions to set data held in a GenomicInteractions object.
show-method | Representation function for GenomicInteractions
sort-method | Sort GenomicInteractions Object
subsetByFeatures | Subset a GenomicInteractions object by features
subsetByFeatures-method | Subset a GenomicInteractions object by features
sum-method | Return the total number of interactions in a GenomicInteractions GIObject
summariseByFeatures | Summary statistics of interactions for a given feature set
summariseByFeatures-method | Summary statistics of interactions for a given feature set
trim-method | Trim a GenomicInteractions object
viewPoint | Virtual 4C viewpoint
[ | Standard subsetting methods for GenomicInteractions objects
[-method | Standard subsetting methods for GenomicInteractions objects