Base Classes for Storing Genomic Link Data
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Documentation for package ‘linkSet’ version 1.1.0
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 |