Package: InteractionSet 1.35.0

Aaron Lun

InteractionSet: Base Classes for Storing Genomic Interaction Data

Provides the GInteractions, InteractionSet and ContactMatrix objects and associated methods for storing and manipulating genomic interaction data from Hi-C and ChIA-PET experiments.

Authors:Aaron Lun [aut, cre], Malcolm Perry [aut], Elizabeth Ing-Simmons [aut]

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InteractionSet.pdf |InteractionSet.html✨
InteractionSet/json (API)
NEWS

# Install 'InteractionSet' in R:
install.packages('InteractionSet', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:InteractionSet-1.35.0(bioc 3.21)InteractionSet-1.34.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

infrastructuredatarepresentationsoftwarehiccpp

7.96 score 36 packages 247 scripts 2.9k downloads 6 mentions 27 exports 30 dependencies

Last updated 2 months agofrom:8c47d4b4de. Checks:OK: 1 NOTE: 5 WARNING: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-win-x86_64NOTENov 29 2024
R-4.5-linux-x86_64NOTENov 29 2024
R-4.4-win-x86_64NOTENov 29 2024
R-4.4-mac-x86_64NOTENov 29 2024
R-4.4-mac-aarch64NOTENov 29 2024
R-4.3-win-x86_64WARNINGNov 29 2024
R-4.3-mac-x86_64WARNINGNov 29 2024
R-4.3-mac-aarch64WARNINGNov 29 2024

Exports:anchorIdsanchorIds<-anchorsappendRegions<-as.matrix<-boundingBoxContactMatrixcountOverlapsdeflatefindOverlapsGInteractionsinflateinteractionsinteractions<-InteractionSetintrachrlinearizelinkOverlapsmakeGInteractionsFromGRangesPairspairdistpairsreduceRegionsregionsregions<-replaceRegions<-swapAnchorsupdateObject

Dependencies:abindaskpassBiobaseBiocGenericscrayoncurlDelayedArraygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6RcppS4ArraysS4VectorsSparseArraySummarizedExperimentsysUCSC.utilsXVectorzlibbioc

Classes for genomic interaction data

Aaron Lun

Rendered frominteractions.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2021-04-16
Started: 2016-04-06

Readme and manuals

Help Manual

Help pageTopics
Get the bounding boxboundingBox boundingBox,GInteractions-method boundingBox,InteractionSet-method
ContactMatrix accessorsanchorIds,ContactMatrix-method anchorIds<-,ContactMatrix-method anchors,ContactMatrix-method anchors<-,ContactMatrix-method appendRegions<-,ContactMatrix-method as.matrix,ContactMatrix-method as.matrix<- as.matrix<-,ContactMatrix-method ContactMatrix-access dim,ContactMatrix-method dimnames,ContactMatrix-method dimnames<-,ContactMatrix,ANY-method dimnames<-,ContactMatrix-method length,ContactMatrix-method reduceRegions,ContactMatrix-method regions,ContactMatrix-method regions<-,ContactMatrix-method replaceRegions<-,ContactMatrix-method show,ContactMatrix-method t,ContactMatrix-method
ContactMatrix class and constructorsContactMatrix ContactMatrix,ANY,GRanges,GRanges,GenomicRanges_OR_missing-method ContactMatrix,ANY,numeric,numeric,GRanges-method ContactMatrix,missing,missing,missing,GenomicRanges_OR_missing-method ContactMatrix-class
Compute linear distances from ContactMatrix objectsContactMatrix-dist intrachr,ContactMatrix-method pairdist,ContactMatrix-method
Find overlaps between GRanges and a ContactMatrixoverlapsAny,ContactMatrix,GInteractions-method overlapsAny,ContactMatrix,GRanges-method overlapsAny,ContactMatrix,GRangesList-method overlapsAny,ContactMatrix,InteractionSet-method
ContactMatrix sorting and orderingContactMatrix-sort duplicated,ContactMatrix-method order,ContactMatrix-method sort,ContactMatrix-method unique,ContactMatrix-method
ContactMatrix subsetting and combiningcbind,ContactMatrix-method ContactMatrix-subset rbind,ContactMatrix-method subset,ContactMatrix-method [,ContactMatrix,ANY,ANY,ANY-method [,ContactMatrix,ANY,ANY-method [,ContactMatrix,ANY-method [<-,ContactMatrix,ANY,ANY,ContactMatrix-method
Convert between classesdeflate deflate,ContactMatrix-method inflate inflate,GInteractions-method inflate,InteractionSet-method
GInteractions class and constructorsGInteractions GInteractions,GRanges,GRanges,GenomicRanges_OR_missing-method GInteractions,missing,missing,GenomicRanges_OR_missing-method GInteractions,numeric,numeric,GRanges-method GInteractions-class ReverseStrictGInteractions-class StrictGInteractions-class
Equivalents of GRanges methodsflank,ContactMatrix-method flank,GInteractions-method flank,InteractionSet-method narrow,ContactMatrix-method narrow,GInteractions-method narrow,InteractionSet-method resize,ContactMatrix-method resize,GInteractions-method resize,InteractionSet-method shift,ContactMatrix-method shift,GInteractions-method shift,InteractionSet-method trim,ContactMatrix-method trim,GInteractions-method trim,InteractionSet-method width,ContactMatrix-method width,GInteractions-method width,InteractionSet-method
Interaction accessors$,GInteractions-method $<-,GInteractions-method anchorIds anchorIds,GInteractions-method anchorIds,InteractionSet-method anchorIds<- anchorIds<-,GInteractions-method anchorIds<-,InteractionSet-method anchorIds<-,ReverseStrictGInteractions-method anchorIds<-,StrictGInteractions-method anchors anchors,GInteractions-method anchors,InteractionSet-method anchors<- anchors<-,GInteractions-method anchors<-,InteractionSet-method anchors<-,ReverseStrictGInteractions-method anchors<-,StrictGInteractions-method appendRegions<- appendRegions<-,GInteractions-method appendRegions<-,InteractionSet-method as.data.frame,GInteractions-method first first,GInteractions-method first,InteractionSet-method interaction-access interactions interactions,InteractionSet-method interactions<- interactions<-,InteractionSet-method length,GInteractions-method mcols,InteractionSet-method mcols<-,InteractionSet-method names,GInteractions-method names,InteractionSet-method names<-,GInteractions-method names<-,InteractionSet-method reduceRegions reduceRegions,GInteractions-method reduceRegions,InteractionSet-method regions regions,GInteractions-method regions,InteractionSet-method regions<- regions<-,GInteractions-method regions<-,InteractionSet-method replaceRegions<- replaceRegions<-,GInteractions-method replaceRegions<-,InteractionSet-method second second,GInteractions-method second,InteractionSet-method seqinfo,GInteractions-method seqinfo,InteractionSet-method seqinfo<-,GInteractions-method seqinfo<-,InteractionSet-method show,GInteractions-method show,InteractionSet-method
Interaction combiningc,GInteractions-method cbind,InteractionSet-method interaction-bind rbind,InteractionSet-method
Interaction comparisonsduplicated,GInteractions-method duplicated,InteractionSet-method interaction-compare match,GInteractions,GInteractions-method match,GInteractions,InteractionSet-method match,InteractionSet,GInteractions-method match,InteractionSet,InteractionSet-method order,GInteractions-method order,InteractionSet-method pcompare,GInteractions,GInteractions-method sort,GInteractions-method sort,InteractionSet-method swapAnchors swapAnchors,GInteractions-method swapAnchors,InteractionSet-method unique,GInteractions-method unique,InteractionSet-method
Get the linear distance for each interactionintrachr intrachr,GInteractions-method intrachr,InteractionSet-method pairdist pairdist,GInteractions-method pairdist,InteractionSet-method
Find overlaps between interactions in one or two dimensionscountOverlaps countOverlaps,GInteractions,GInteractions-method countOverlaps,GInteractions,InteractionSet-method countOverlaps,GInteractions,missing-method countOverlaps,GInteractions,Vector-method countOverlaps,InteractionSet,GInteractions-method countOverlaps,InteractionSet,InteractionSet-method countOverlaps,InteractionSet,missing-method countOverlaps,InteractionSet,Vector-method countOverlaps,Vector,GInteractions-method countOverlaps,Vector,InteractionSet-method findOverlaps findOverlaps,GInteractions,GInteractions-method findOverlaps,GInteractions,InteractionSet-method findOverlaps,GInteractions,missing-method findOverlaps,GInteractions,Vector-method findOverlaps,InteractionSet,GInteractions-method findOverlaps,InteractionSet,InteractionSet-method findOverlaps,InteractionSet,missing-method findOverlaps,InteractionSet,Vector-method findOverlaps,Vector,GInteractions-method findOverlaps,Vector,InteractionSet-method Interaction-overlaps overlapsAny overlapsAny,GInteractions,GInteractions-method overlapsAny,GInteractions,InteractionSet-method overlapsAny,GInteractions,missing-method overlapsAny,GInteractions,Vector-method overlapsAny,InteractionSet,GInteractions-method overlapsAny,InteractionSet,InteractionSet-method overlapsAny,InteractionSet,missing-method overlapsAny,InteractionSet,Vector-method overlapsAny,Vector,GInteractions-method overlapsAny,Vector,InteractionSet-method subsetByOverlaps subsetByOverlaps,GInteractions,GInteractions-method subsetByOverlaps,GInteractions,InteractionSet-method subsetByOverlaps,GInteractions,Vector-method subsetByOverlaps,InteractionSet,GInteractions-method subsetByOverlaps,InteractionSet,InteractionSet-method subsetByOverlaps,InteractionSet,Vector-method subsetByOverlaps,Vector,GInteractions-method subsetByOverlaps,Vector,InteractionSet-method
Interaction subsetting and combininginteraction-subset subset,InteractionSet-method [,InteractionSet,ANY,ANY,ANY-method [,InteractionSet,ANY,ANY-method [,InteractionSet,ANY-method [<-,GInteractions,ANY,GInteractions-method [<-,InteractionSet,ANY,ANY,InteractionSet-method
InteractionSet class and constructorsInteractionSet InteractionSet,ANY,GInteractions-method InteractionSet,missing,missing-method InteractionSet-class
Linearize 2D interactions into 1D rangeslinearize linearize,GInteractions,GRanges-method linearize,GInteractions,numeric-method linearize,InteractionSet,GRanges-method linearize,InteractionSet,numeric-method
Link overlapping regionslinkOverlaps linkOverlaps,GInteractions,Hits,Hits-method linkOverlaps,GInteractions,Hits,missing-method linkOverlaps,GInteractions,Vector,missing-method linkOverlaps,GInteractions,Vector,Vector-method linkOverlaps,InteractionSet,Hits,Hits-method linkOverlaps,InteractionSet,Hits,missing-method linkOverlaps,InteractionSet,Vector,missing-method linkOverlaps,InteractionSet,Vector,Vector-method
Extract paired rangesmakeGInteractionsFromGRangesPairs pairs pairs,GInteractions-method pairs,InteractionSet-method
Update a GInteractions objectupdateObject updateObject,GInteractions-method