Package index • linkSet

All functions

Convert(<GInteractions>) Convert(<data.frame>) Convert(<Pairs>) Convert(<ANY>) readvalidPairs(): Convert GInteractions to linkSet

annotateInter(<linkSet>): Annotate linkSet with inter/intra chromosome interactions

annotatePromoter(<linkSet>): Annotate the link set with txDb. Give a gene list, and return a

as.GInteractions(): Convert to GInteractions

as.data.frame(<linkSet>): coerce linkSet to DataFrame

baitGInteractions(): Convert GInteractions to linkSet with bait annotations

character_Or_missing-class: Character or Missing Class Union

clean_unused_regions(): Clean Unused Regions in a linkSet Object

countInteractibility(): Count bait and oe interactibility

countInteractions(): Count Bait and Other End Interactions

crossGeneEnhancer(<linkSet>): Cross gene enhancer

diagnoseLinkSet(<linkSet>): Diagnose the linkSet object, return barplot of inter/intra interaction and distance distribution

.check.split.data.numerical.fit(): check.split.data.numerical.fit

exportInterBed(): Export linkSet to interBed format

exportWashU(): Export linkSet to WashU browser format

filterLinks(<linkSet>): Filter links for further analysis

geom_linkset(): Add Genome Links to Coverage Plot

geom_range(): Plot genomic ranges

linkExample: Example linkSet Object

trim(<linkSet>) resize(<linkSet>) resizeRegions(<linkSet>) narrow(<linkSet>) narrowRegions(<linkSet>) shift(<linkSet>) shiftRegions(<linkSet>) flank(<linkSet>) flankRegions(<linkSet>) promoters(<linkSet>) promoterRegions(<linkSet>) width(<linkSet>) reduce(<linkSet>): linkSet-GRange-Methods

linkSet(<GRanges>,<GRanges>,<character_Or_missing>): Create a linkSet object from input data

`bait<-`() `regions<-`() `anchor1<-`() `anchor2<-`() `unchecked_regions<-`() anchor1(<linkSet>) anchor2(<linkSet>) regions(<linkSet>) seqinfo(<linkSet>) anchorIds(<linkSet>) anchors(<linkSet>) first(<linkSet>) second(<linkSet>) bait(<linkSet>) oe(<linkSet>) regionsBait(<linkSet>) `unchecked_anchor1<-`(<linkSet>) `unchecked_anchor2<-`(<linkSet>) `regionsBait<-`(<linkSet>) `oe<-`(<linkSet>) `$`(<linkSet>) `$<-`(<linkSet>) names(<linkSet>) `names<-`(<linkSet>): linkSet-accessors

linkSet(<character>,<GRanges>,<character_Or_missing>): Create a linkSet object from input data

linkSet-class LinkSet: LinkSet object

subsetBait(<linkSet>) subsetBaitRegion(<linkSet>) subsetOE(<linkSet>): Subset linkSet object based on bait names

theme_linkset() theme_range(): linkSet-theme

linkSet: linkSet: Base Classes for Storing Genomic Link Data

`oe<-`(): Set Other End (OE) Anchors

orderLinks(<linkSet>): Order linkSet by mcols

pairdist(<linkSet>): Calculate the distance between bait and the other end

plotBaits(): Plot Baits

plot_genomic_ranges(<linkSet>): plot genomic ranges and links

reduceRegions(): Reduce Regions in a linkSet Object

`regionsBait<-`(): Set Bait Regions

run_chicane(): Run ChICANE Analysis

show(<linkSet>): Display detailed information about a linkSet object

showLinkSet(): Show linkSet Object Details

withTxDb(): Database Operation with Connection Management