annotateInter,linkSet-method
                        Annotate linkSet with inter/intra chromosome
                        interactions
annotatePromoter,linkSet-method
                        Annotate the link set with txDb. Give a gene
                        list, and return a
as.data.frame,linkSet-method
                        coerce linkSet to DataFrame
as.GInteractions        Convert to GInteractions
bait<-                  linkSet-accessors
baitGInteractions       Convert GInteractions to linkSet with bait
                        annotations
character_Or_missing-class
                        Character or Missing Class Union
cleanUnusedRegions      Clean Unused Regions
Convert,GInteractions-method
                        Convert GInteractions to linkSet
countInteractibility    Count bait and oe interactibility
countInteractions       Count Bait and Other End Interactions
crossGeneEnhancer,linkSet-method
                        Cross gene enhancer
diagnoseLinkSet,linkSet-method
                        Diagnose the linkSet object, return barplot of
                        inter/intra interaction and distance
                        distribution
Embryo_body             Embryo Body BED File
exportInterBed          Export linkSet to interBed format
exportWashU             Export linkSet to WashU browser format
filterLinks,linkSet-method
                        Filter links for further analysis
geom_linkset            Add Genome Links to Coverage Plot
linkExample             Example linkSet Object
linkSet                 linkSet: Base Classes for Storing Genomic Link
                        Data
linkSet-class           LinkSet object
linkSet,character,GRanges,character_Or_missing-method
                        Create a linkSet object from input data
linkSet,GRanges,GRanges,character_Or_missing-method
                        Create a linkSet object from input data
oe<-                    Set Other End (OE) Anchors
orderLinks,linkSet-method
                        Order linkSet by mcols
pairdist,linkSet-method
                        Calculate the distance between bait and the
                        other end
plotBaits               Plot Baits
plotGenomicRanges       Plot Genomic Ranges
plotGenomicRanges,linkSet-method
                        Plot genomic ranges for linkSet objects
reduceRegions           Reduce Regions in a linkSet Object
regionsBait<-           Set Bait Regions
run_chicane             Run ChICANE Analysis
show,linkSet-method     Display detailed information about a linkSet
                        object
showLinkSet             Show linkSet Object Details
subsetBait,linkSet-method
                        Subset linkSet object based on bait names
themeLinkset            Theme for linkSet plots
themeRange              Theme for genomic range plots
trim,linkSet-method     linkSet-GRange-Methods
withTxDb                Database Operation with Connection Management
