R package for handling genomic interaction data


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Documentation for package ‘GenomicInteractions’ version 1.20.3

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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
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.
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.
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