# Generated by roxygen2: do not edit by hand

S3method(ggplot_add,interSet)
export("anchor1<-")
export("anchor2<-")
export("bait<-")
export("oe<-")
export("regions<-")
export("regionsBait<-")
export("unchecked_regions<-")
export(Convert)
export(anchor1)
export(anchor2)
export(anchorIds)
export(anchors)
export(annotateInter)
export(annotatePromoter)
export(as.GInteractions)
export(bait)
export(baitGInteractions)
export(cleanUnusedRegions)
export(clean_unused_regions)
export(countInteractibility)
export(countInteractions)
export(crossGeneEnhancer)
export(diagnoseLinkSet)
export(exportInterBed)
export(exportWashU)
export(filterLinks)
export(flankRegions)
export(geom_linkset)
export(linkSet)
export(narrowRegions)
export(oe)
export(orderLinks)
export(pairdist)
export(plotBaits)
export(plotGenomicRanges)
export(plot_genomic_ranges)
export(promoterRegions)
export(readvalidPairs)
export(reduceRegions)
export(regions)
export(regionsBait)
export(resizeRegions)
export(run_chicane)
export(shiftRegions)
export(showLinkSet)
export(subsetBait)
export(subsetBaitRegion)
export(subsetOE)
export(themeLinkset)
export(themeRange)
export(withTxDb)
exportClasses(character_Or_missing)
exportClasses(linkSet)
exportMethods("bait<-")
exportMethods("names<-")
exportMethods("oe<-")
exportMethods("regionsBait<-")
exportMethods("unchecked_regions<-")
exportMethods(Convert)
exportMethods(anchor1)
exportMethods(anchor2)
exportMethods(anchorIds)
exportMethods(anchors)
exportMethods(annotateInter)
exportMethods(annotatePromoter)
exportMethods(as.GInteractions)
exportMethods(as.data.frame)
exportMethods(bait)
exportMethods(baitGInteractions)
exportMethods(cleanUnusedRegions)
exportMethods(clean_unused_regions)
exportMethods(countInteractibility)
exportMethods(countInteractions)
exportMethods(crossGeneEnhancer)
exportMethods(diagnoseLinkSet)
exportMethods(exportInterBed)
exportMethods(exportWashU)
exportMethods(filterLinks)
exportMethods(first)
exportMethods(flank)
exportMethods(flankRegions)
exportMethods(geom_linkset)
exportMethods(linkSet)
exportMethods(names)
exportMethods(narrow)
exportMethods(narrowRegions)
exportMethods(oe)
exportMethods(orderLinks)
exportMethods(pairdist)
exportMethods(plotGenomicRanges)
exportMethods(plot_genomic_ranges)
exportMethods(promoterRegions)
exportMethods(promoters)
exportMethods(reduce)
exportMethods(reduceRegions)
exportMethods(regions)
exportMethods(regionsBait)
exportMethods(resize)
exportMethods(resizeRegions)
exportMethods(run_chicane)
exportMethods(second)
exportMethods(seqinfo)
exportMethods(shift)
exportMethods(shiftRegions)
exportMethods(show)
exportMethods(showLinkSet)
exportMethods(subsetBait)
exportMethods(subsetBaitRegion)
exportMethods(subsetOE)
exportMethods(trim)
exportMethods(width)
exportMethods(withTxDb)
import(data.table)
importClassesFrom(GenomicRanges,GRanges)
importFrom(BiocGenerics,end)
importFrom(BiocGenerics,start)
importFrom(BiocGenerics,width)
importFrom(GenomeInfoDb,seqinfo)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,flank)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,narrow)
importFrom(GenomicRanges,promoters)
importFrom(GenomicRanges,ranges)
importFrom(GenomicRanges,reduce)
importFrom(GenomicRanges,resize)
importFrom(GenomicRanges,seqnames)
importFrom(GenomicRanges,start)
importFrom(GenomicRanges,strand)
importFrom(GenomicRanges,trim)
importFrom(IRanges,IRanges)
importFrom(IRanges,subsetByOverlaps)
importFrom(Organism.dplyr,select)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,Rle)
importFrom(S4Vectors,make_zero_col_DFrame)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,showAsCell)
importFrom(S4Vectors,subjectHits)
importFrom(data.table,":=")
importFrom(foreach,"%dopar%")
importFrom(ggplot2,aes_string)
importFrom(ggplot2,coord_cartesian)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,expansion)
importFrom(ggplot2,geom_curve)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggplot_add)
importFrom(ggplot2,labs)
importFrom(ggplot2,margin)
importFrom(ggplot2,scale_color_gradientn)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,theme_void)
importFrom(grid,arrow)
importFrom(grid,unit)
importFrom(iterators,icount)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,setClass)
importFrom(methods,setGeneric)
importFrom(methods,setMethod)
importFrom(methods,show)
importFrom(patchwork,plot_layout)
importFrom(patchwork,wrap_plots)
importFrom(rlang,.data)
importFrom(scales,rescale)
importFrom(stats,logLik)
importFrom(stats,setNames)
importFrom(utils,getFromNamespace)
importFrom(utils,read.table)
importFrom(utils,write.table)
