API for GenomicInteractions
Utilities for handling genomic interaction data

Global functions
.exportName	Source code
.getNames	Source code
.getScore	Source code
.get_gr_names	Source code
.importHicLib	Man page Source code
.importHomer	Man page Source code
.isEqualSeqInfo	Source code
.makeRelativeVP	Source code
.process.chr	Source code
.processChiapetName	Man page Source code
.readBam	Man page Source code
.readTwoBams	Man page Source code
.validateInput	Man page Source code
GenomicInteractions	Man page
GenomicInteractions,ANY,ANY,ANY-method	Man page
GenomicInteractions,GInteractions,ANY,ANY-method	Man page
GenomicInteractions,GInteractions,numeric,ANY-method	Man page
GenomicInteractions,GRanges,GRanges,GenomicRanges_OR_missing-met	Man page
GenomicInteractions,GRanges,GRanges,numeric-method	Man page
GenomicInteractions,missing,missing,GenomicRanges_OR_missing-met	Man page
GenomicInteractions,numeric,numeric,GRanges-method	Man page
GenomicInteractions-class	Man page
GenomicInteractions-package	Man page
InteractionHelpers	Man page
InteractionTrack	Man page Source code
InteractionTrack-class	Man page
anchorOne	Man page
anchorOne,GInteractions-method	Man page
anchorTwo	Man page
anchorTwo,GInteractions-method	Man page
annotateInteractions	Man page
annotateInteractions,GInteractions,list-method	Man page
annotateRegions	Man page
annotateRegions,GInteractions,character,vector-method	Man page
annotationFeatures	Man page
annotationFeatures,GInteractions-method	Man page
asBED,GInteractions-method	Man page
availableDisplayPars	Man page Source code
calculateDistances	Man page
calculateDistances,GInteractions-method	Man page
capitalize	Source code
categoriseInteractions	Man page Source code
countsBetweenAnchors	Man page
countsBetweenAnchors,GInteractions,GRanges-method	Man page
description,GInteractions-method	Man page
description<-,GInteractions,ANY-method	Man page
export.bed12	Man page
export.bed12,GInteractions-method	Man page
export.bedpe	Man page
export.bedpe,GInteractions-method	Man page
export.chiasig	Man page
export.chiasig,GInteractions-method	Man page
export.igraph	Man page
export.igraph,GInteractions-method	Man page
get_binom_ligation_threshold	Man page Source code
get_self_ligation_threshold	Man page Source code
getters	Man page
hg19.refseq.transcripts	Man page
hic_example_data	Man page
interactionCounts	Man page
interactionCounts,GInteractions-method	Man page
interactionCounts<-	Man page
interactionCounts<-,GInteractions-method	Man page
is.cis	Man page
is.cis,GInteractions-method	Man page
is.dd	Man page
is.dd,GInteractions-method	Man page
is.dt	Man page
is.dt,GInteractions-method	Man page
is.pd	Man page
is.pd,GInteractions-method	Man page
is.pp	Man page
is.pp,GInteractions-method	Man page
is.pt	Man page
is.pt,GInteractions-method	Man page
is.trans	Man page
is.trans,GInteractions-method	Man page
is.tt	Man page
is.tt,GInteractions-method	Man page
isInteractionType	Man page
isInteractionType,GInteractions-method	Man page
makeGenomicInteractionsFromFile	Man page Source code
mm9_refseq_promoters	Man page
name	Man page
name,GInteractions-method	Man page
name<-	Man page
name<-,GInteractions-method	Man page
plotAvgViewpoint	Man page Source code
plotCisTrans	Man page Source code
plotCounts	Man page Source code
plotDists	Man page Source code
plotInteractionAnnotations	Man page Source code
plotSummaryStats	Man page Source code
plotViewpoint	Man page Source code
removeDups	Man page Source code
resetAnnotations	Man page
resetAnnotations,GInteractions-method	Man page
sameStrand	Man page Source code
setters	Man page
subsetByFeatures	Man page
subsetByFeatures,GInteractions,GRanges,missing-method	Man page
subsetByFeatures,GInteractions,GRangesList,missing-method	Man page
subsetByFeatures,GInteractions,character,character-method	Man page
sum,GInteractions-method	Man page
summariseByFeaturePairs	Man page
summariseByFeaturePairs,GInteractions-method	Man page
summariseByFeatures	Man page
summariseByFeatures,GInteractions-method	Man page
thymus_enh	Man page
updateObject,GenomicInteractions-method	Man page
viewPoint	Man page Source code