# Base Classes for Storing Genomic Link Data

## Documentation for package ‘linkSet’ version 1.0.0

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

## Help Pages

A B C D E F G L N O P R S T U W misc

## -- A --

anchor1 | linkSet-accessors
anchor1-method | linkSet-accessors
anchor1<- | linkSet-accessors
anchor2 | linkSet-accessors
anchor2-method | linkSet-accessors
anchor2<- | linkSet-accessors
anchorIds | linkSet-accessors
anchorIds-method | linkSet-accessors
anchors | linkSet-accessors
anchors-method | linkSet-accessors
annotateInter | Annotate linkSet with inter/intra chromosome interactions
annotateInter-method | Annotate linkSet with inter/intra chromosome interactions
annotatePromoter | Annotate the link set with txDb. Give a gene list, and return a
annotatePromoter-method | Annotate the link set with txDb. Give a gene list, and return a
as.data.frame-method | coerce linkSet to DataFrame
as.GInteractions | Convert to GInteractions
as.GInteractions-method | Convert to GInteractions

## -- B --

bait | linkSet-accessors
bait-method | linkSet-accessors
bait<- | linkSet-accessors
bait<--method | linkSet-accessors
baitGInteractions | Convert GInteractions to linkSet with bait annotations
baitGInteractions-method | Convert GInteractions to linkSet with bait annotations

## -- C --

character_Or_missing-class | Character or Missing Class Union
cleanUnusedRegions | Clean Unused Regions
cleanUnusedRegions-method | Clean Unused Regions
clean_unused_regions | Clean Unused Regions
clean_unused_regions-method | Clean Unused Regions
Convert | Convert GInteractions to linkSet
Convert-method | Convert GInteractions to linkSet
countBaitOe | Count Bait and Other End Interactions
countInteractibility | Count bait and oe interactibility
countInteractibility-method | Count bait and oe interactibility
countInteractions | Count Bait and Other End Interactions
countInteractions-method | Count Bait and Other End Interactions
crossGeneEnhancer | Cross gene enhancer
crossGeneEnhancer-method | Cross gene enhancer

## -- D --

diagnoseLinkSet | Diagnose the linkSet object, return barplot of inter/intra interaction and distance distribution
diagnoseLinkSet-method | Diagnose the linkSet object, return barplot of inter/intra interaction and distance distribution

## -- E --

Embryo_body | Embryo Body BED File
exportInterBed | Export linkSet to interBed format
exportInterBed-method | Export linkSet to interBed format
exportWashU | Export linkSet to WashU browser format
exportWashU-method | Export linkSet to WashU browser format

## -- F --

filterLinks | Filter links for further analysis
filterLinks-method | Filter links for further analysis
first | linkSet-accessors
first-method | linkSet-accessors
flank | linkSet-GRange-Methods
flank-method | linkSet-GRange-Methods
flankRegions | linkSet-GRange-Methods
flankRegions-method | linkSet-GRange-Methods

## -- G --

geom_linkset | Add Genome Links to Coverage Plot
geom_linkset-method | Add Genome Links to Coverage Plot

## -- L --

linkExample | Example linkSet Object
LinkSet | LinkSet object
linkSet | linkSet: Base Classes for Storing Genomic Link Data
linkSet-class | LinkSet object
linkSet-method | Create a linkSet object from input data
linkSet-method | Create a linkSet object from input data

## -- N --

names | linkSet-accessors
names-method | linkSet-accessors
names<- | linkSet-accessors
names<--method | linkSet-accessors
narrow | linkSet-GRange-Methods
narrow-method | linkSet-GRange-Methods
narrowRegions | linkSet-GRange-Methods
narrowRegions-method | linkSet-GRange-Methods

## -- O --

oe | linkSet-accessors
oe-method | linkSet-accessors
oe<- | Set Other End (OE) Anchors
oe<--method | linkSet-accessors
orderLinks | Order linkSet by mcols
orderLinks-method | Order linkSet by mcols

## -- P --

pairdist | Calculate the distance between bait and the other end
pairdist-method | Calculate the distance between bait and the other end
plotBaits | Plot Baits
plotGenomicRanges | Plot Genomic Ranges
plotGenomicRanges-method | Plot genomic ranges for linkSet objects
plot_genomic_ranges | Plot Genomic Ranges
plot_genomic_ranges-method | Plot Genomic Ranges
promoterRegions | linkSet-GRange-Methods
promoterRegions-method | linkSet-GRange-Methods
promoters | linkSet-GRange-Methods
promoters-method | linkSet-GRange-Methods

## -- R --

readvalidPairs | Convert GInteractions to linkSet
reduce | linkSet-GRange-Methods
reduce-method | linkSet-GRange-Methods
reduceRegions | Reduce Regions in a linkSet Object
reduceRegions-method | Reduce Regions in a linkSet Object
regions | linkSet-accessors
regions-method | linkSet-accessors
regions<- | linkSet-accessors
regions<--method | linkSet-accessors
regionsBait | linkSet-accessors
regionsBait-method | linkSet-accessors
regionsBait<- | Set Bait Regions
regionsBait<--method | linkSet-accessors
resize | linkSet-GRange-Methods
resize-method | linkSet-GRange-Methods
resizeRegions | linkSet-GRange-Methods
resizeRegions-method | linkSet-GRange-Methods
run_chicane | Run ChICANE Analysis
run_chicane-method | Run ChICANE Analysis

## -- S --

second | linkSet-accessors
second-method | linkSet-accessors
seqinfo | linkSet-accessors
seqinfo-method | linkSet-accessors
shift | linkSet-GRange-Methods
shift-method | linkSet-GRange-Methods
shiftRegions | linkSet-GRange-Methods
shiftRegions-method | linkSet-GRange-Methods
show-method | Display detailed information about a linkSet object
showLinkSet | Show linkSet Object Details
showLinkSet-method | Show linkSet Object Details
subsetBait | Subset linkSet object based on bait names
subsetBait-method | Subset linkSet object based on bait names
subsetBaitRegion | Subset linkSet object based on bait names
subsetBaitRegion-method | Subset linkSet object based on bait names
subsetOE | Subset linkSet object based on bait names
subsetOE-method | Subset linkSet object based on bait names

## -- T --

themeLinkset | Theme for linkSet plots
themeRange | Theme for genomic range plots
trim | linkSet-GRange-Methods
trim-method | linkSet-GRange-Methods

## -- U --

unchecked_anchor1 | linkSet-accessors
unchecked_anchor1<--method | linkSet-accessors
unchecked_anchor2 | linkSet-accessors
unchecked_anchor2<--method | linkSet-accessors
unchecked_regions | linkSet-accessors
unchecked_regions<- | linkSet-accessors
unchecked_regions<--method | linkSet-accessors

## -- W --

width | linkSet-GRange-Methods
width-method | linkSet-GRange-Methods
withTxDb | Database Operation with Connection Management
withTxDb-method | Database Operation with Connection Management

## -- misc --

$ | linkSet-accessors
$-method | linkSet-accessors
$<--method | linkSet-accessors