linkSet-package	linkSet-package
$	linkSet-accessors
$,linkSet-method	linkSet-accessors
$<-,linkSet-method	linkSet-accessors
anchor1	linkSet-accessors
anchor1,linkSet-method	linkSet-accessors
anchor1<-	linkSet-accessors
anchor2	linkSet-accessors
anchor2,linkSet-method	linkSet-accessors
anchor2<-	linkSet-accessors
anchorIds	linkSet-accessors
anchorIds,linkSet-method	linkSet-accessors
anchors	linkSet-accessors
anchors,linkSet-method	linkSet-accessors
annotateInter	annotateInter-linkSet-method
annotateInter,linkSet-method	annotateInter-linkSet-method
annotatePromoter	annotatePromoter-linkSet-method
annotatePromoter,linkSet-method	annotatePromoter-linkSet-method
as.data.frame,linkSet-method	as.data.frame-linkSet-method
as.GInteractions	as.GInteractions
as.GInteractions,linkSet-method	as.GInteractions
bait	linkSet-accessors
bait,linkSet-method	linkSet-accessors
bait<-	linkSet-accessors
bait<-,linkSet-method	linkSet-accessors
baitGInteractions	baitGInteractions
baitGInteractions,GInteractions,GRanges,GRanges-method	baitGInteractions
character_Or_missing-class	character_Or_missing-class
checkModelNumericalFit	chicane
checkPackages	checkPackages
checkSplitDataNumericalFit	checkSplitDataNumericalFit
cleanUnusedRegions	cleanUnusedRegions
cleanUnusedRegions,linkSet-method	cleanUnusedRegions
clean_unused_regions	cleanUnusedRegions
clean_unused_regions,linkSet-method	cleanUnusedRegions
Convert	Convert
Convert,ANY-method	Convert
Convert,data.frame-method	Convert
Convert,GInteractions-method	Convert
Convert,Pairs-method	Convert
convertToGrange	convertToGrange
countBaitOe	countInteractions
countInteractibility	countInteractibility
countInteractibility,linkSet-method	countInteractibility
countInteractions	countInteractions
countInteractions,linkSet-method	countInteractions
createSampleLinkSet	createSampleLinkSet
crossGeneEnhancer	crossGeneEnhancer-linkSet-method
crossGeneEnhancer,linkSet-method	crossGeneEnhancer-linkSet-method
diagnoseLinkSet	diagnoseLinkSet-linkSet-method
diagnoseLinkSet,linkSet-method	diagnoseLinkSet-linkSet-method
Embryo_body	Embryo_body
enforceOrder	enforceOrder
exportInterBed	exportInterBed
exportInterBed,linkSet-method	exportInterBed
exportToLinkSet	exportToLinkSet
exportWashU	exportWashU
exportWashU,linkSet-method	exportWashU
filterLinks	filterLinks-linkSet-method
filterLinks,linkSet-method	filterLinks-linkSet-method
first	linkSet-accessors
first,linkSet-method	linkSet-accessors
fitGlm	chicane
flank	linkSet-GRange-Methods
flank,linkSet-method	linkSet-GRange-Methods
flankRegions	linkSet-GRange-Methods
flankRegions,linkSet-method	linkSet-GRange-Methods
geom_linkset	geom_linkset
geom_linkset,linkSet-method	geom_linkset
getDistOutput	getDistOutput
isGlmNbMaxiterWarning	chicane
isGlmNbThetaError	chicane
isGlmNbThetaWarning	chicane
linkExample	linkExample
LinkSet	linkSet-class
linkSet	linkSet
linkSet,character,GRanges,character_Or_missing-method	linkSet-character-GRanges-character_Or_missing-method
linkSet,GRanges,GRanges,character_Or_missing-method	linkSet-GRanges-GRanges-character_Or_missing-method
linkSet-class	linkSet-class
modelRowsSanityCheck	chicane
multipleTestingCorrect	chicane
names	linkSet-accessors
names,linkSet-method	linkSet-accessors
names<-	linkSet-accessors
names<-,linkSet-method	linkSet-accessors
narrow	linkSet-GRange-Methods
narrow,linkSet-method	linkSet-GRange-Methods
narrowRegions	linkSet-GRange-Methods
narrowRegions,linkSet-method	linkSet-GRange-Methods
oe	linkSet-accessors
oe,linkSet-method	linkSet-accessors
oe<-	oe-set
oe<-,linkSet-method	linkSet-accessors
orderLinks	orderLinks-linkSet-method
orderLinks,linkSet-method	orderLinks-linkSet-method
pairdist	pairdist-linkSet-method
pairdist,linkSet-method	pairdist-linkSet-method
pasteAnchor	pasteAnchor
plotBaits	plotBaits
plotGenomicRanges	plotGenomicRanges
plotGenomicRanges,linkSet-method	plotGenomicRanges-linkSet-method
plot_genomic_ranges	plotGenomicRanges
plot_genomic_ranges,linkSet-method	plotGenomicRanges
promoterRegions	linkSet-GRange-Methods
promoterRegions,linkSet-method	linkSet-GRange-Methods
promoters	linkSet-GRange-Methods
promoters,linkSet-method	linkSet-GRange-Methods
readvalidPairs	Convert
reduce	linkSet-GRange-Methods
reduce,linkSet-method	linkSet-GRange-Methods
reduceRegions	reduceRegions
reduceRegions,linkSet-method	reduceRegions
regions	linkSet-accessors
regions,linkSet-method	linkSet-accessors
regions<-	linkSet-accessors
regions<-,linkSet-method	linkSet-accessors
regionsBait	linkSet-accessors
regionsBait,linkSet-method	linkSet-accessors
regionsBait<-	regionsBait-set
regionsBait<-,linkSet-method	linkSet-accessors
resize	linkSet-GRange-Methods
resize,linkSet-method	linkSet-GRange-Methods
resizeRegions	linkSet-GRange-Methods
resizeRegions,linkSet-method	linkSet-GRange-Methods
run_chicane	run_chicane
run_chicane,linkSet-method	run_chicane
second	linkSet-accessors
second,linkSet-method	linkSet-accessors
seqinfo	linkSet-accessors
seqinfo,linkSet-method	linkSet-accessors
shift	linkSet-GRange-Methods
shift,linkSet-method	linkSet-GRange-Methods
shiftRegions	linkSet-GRange-Methods
shiftRegions,linkSet-method	linkSet-GRange-Methods
show,linkSet-method	show
showLinkSet	showLinkSet
showLinkSet,linkSet-method	showLinkSet
smartSplit	chicane
subsetBait	linkSet-subset-methods
subsetBait,linkSet-method	linkSet-subset-methods
subsetBaitRegion	linkSet-subset-methods
subsetBaitRegion,linkSet-method	linkSet-subset-methods
subsetOE	linkSet-subset-methods
subsetOE,linkSet-method	linkSet-subset-methods
themeLinkset	themeLinkset
themeRange	themeRange
trim	linkSet-GRange-Methods
trim,linkSet-method	linkSet-GRange-Methods
unchecked_anchor1	linkSet-accessors
unchecked_anchor1<-	unchecked_anchor1-set
unchecked_anchor1<-,linkSet-method	linkSet-accessors
unchecked_anchor2	linkSet-accessors
unchecked_anchor2<-	unchecked_anchor2-set
unchecked_anchor2<-,linkSet-method	linkSet-accessors
unchecked_regions	linkSet-accessors
unchecked_regions<-	linkSet-accessors
unchecked_regions<-,linkSet-method	linkSet-accessors
verifyInteractionData	chicane
verifyLinkSet	chicane
width	linkSet-GRange-Methods
width,linkSet-method	linkSet-GRange-Methods
withTxDb	withTxDb
withTxDb,character,function-method	withTxDb
