Package index • linkSet

All functions

Convert(): Convert different object types 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.data.frame(<linkSet>): coerce linkSet to DataFrame

baitGInteractions(<GInteractions>,<GRanges>,<GRanges>): Convert GInteractions with bait range and oe ranges to linkSet

countInteractions(<linkSet>): Make Repeated Interactions Unique and Count Repetitions

crossGeneEnhancer(<linkSet>): Cross gene enhancer

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

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

geom_linkset(<linkSet>): Add Genome Links to Coverage Plot.

geom_range(): Plot genomic ranges

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

anchor1(<linkSet>) anchor2(<linkSet>) regions(<linkSet>) seqinfo(<linkSet>): linkSet-accessors

linkSet-class linkSet LinkSet: LinkSet object

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

linkSet: linkSet: Base Classes for Storing Genomic Link Data

orderLinks(<linkSet>): Order linkSet by mcols

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

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

readvalidPairs(): Read validPairs file to GInteractions

reduceRegions(<linkSet>): Reduce a linkSet object