Introduction | Description of the GInteractions class | Construction | Getters | Setters | Subsetting and combining | Sorting, duplication and matching | Distance calculations | Overlap methods | Linking sets of regions | Finding the bounding box | Enforcing anchor ordering in StrictGInteractions | Description of the InteractionSet class | Other methods | Description of the ContactMatrix class | Sorting and duplication | Distance calculation | Converting between classes | Inflating a GInteractions into a ContactMatrix | Deflating a ContactMatrix into an InteractionSet | Linearizing an InteractionSet into a RangedSummarizedExperiment | Summary
Package: InteractionSet 1.41.0
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:
InteractionSet_1.41.0.tar.gz
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InteractionSet_1.41.0.tgz(r-4.6-x86_64)InteractionSet_1.41.0.tgz(r-4.6-arm64)InteractionSet_1.41.0.tgz(r-4.5-x86_64)InteractionSet_1.41.0.tgz(r-4.5-arm64)
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InteractionSet_1.41.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
InteractionSet/json (API)
| # Install 'InteractionSet' in R: |
| install.packages('InteractionSet', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:InteractionSet-1.41.0(bioc 3.24)InteractionSet-1.40.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
infrastructuredatarepresentationsoftwarehiccpp
Last updated from:275c24c965. Checks:12 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 180 | ||
| linux-devel-arm64 | NOTE | 315 | ||
| linux-devel-x86_64 | NOTE | 327 | ||
| source / vignettes | OK | 221 | ||
| linux-release-arm64 | NOTE | 328 | ||
| linux-release-x86_64 | NOTE | 355 | ||
| macos-release-arm64 | NOTE | 375 | ||
| macos-release-x86_64 | NOTE | 730 | ||
| macos-oldrel-arm64 | NOTE | 177 | ||
| macos-oldrel-x86_64 | NOTE | 729 | ||
| windows-devel | NOTE | 346 | ||
| windows-release | NOTE | 329 | ||
| windows-oldrel | NOTE | 305 | ||
| wasm-release | OK | 265 |
Exports:anchorIdsanchorIds<-anchorsappendRegions<-as.matrix<-boundingBoxContactMatrixcountOverlapsdeflatefindOverlapsGInteractionsinflateinteractionsinteractions<-InteractionSetintrachrlinearizelinkOverlapsmakeGInteractionsFromGRangesPairsoverlapsAnypairdistpairsreduceRegionsregionsregions<-replaceRegions<-seqinfoseqinfo<-swapAnchorsupdateObject
Dependencies:abindBiobaseBiocGenericsDelayedArraygenericsGenomicRangesIRangeslatticeMatrixMatrixGenericsmatrixStatsRcppS4ArraysS4VectorsSeqinfoSparseArraySummarizedExperimentXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Get the bounding box | boundingBox boundingBox,GInteractions-method boundingBox,InteractionSet-method |
| ContactMatrix accessors | anchorIds,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 seqinfo,ContactMatrix-method seqinfo<-,ContactMatrix-method show,ContactMatrix-method t,ContactMatrix-method |
| ContactMatrix class and constructors | ContactMatrix 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 objects | ContactMatrix-dist intrachr,ContactMatrix-method pairdist,ContactMatrix-method |
| Find overlaps between GRanges and a ContactMatrix | overlapsAny,ContactMatrix,GInteractions-method overlapsAny,ContactMatrix,InteractionSet-method overlapsAny,ContactMatrix,Vector-method |
| ContactMatrix sorting and ordering | ContactMatrix-sort duplicated,ContactMatrix-method order,ContactMatrix-method sort,ContactMatrix-method unique,ContactMatrix-method |
| ContactMatrix subsetting and combining | cbind,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 classes | deflate deflate,ContactMatrix-method inflate inflate,GInteractions-method inflate,InteractionSet-method |
| GInteractions class and constructors | GInteractions 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 methods | flank,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 combining | c,GInteractions-method cbind,InteractionSet-method interaction-bind rbind,InteractionSet-method |
| Interaction comparisons | duplicated,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 interaction | intrachr intrachr,GInteractions-method intrachr,InteractionSet-method pairdist pairdist,GInteractions-method pairdist,InteractionSet-method |
| Find overlaps between interactions in one or two dimensions | countOverlaps 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 combining | interaction-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 constructors | InteractionSet InteractionSet,ANY,GInteractions-method InteractionSet,missing,missing-method InteractionSet-class |
| Linearize 2D interactions into 1D ranges | linearize linearize,GInteractions,GRanges-method linearize,GInteractions,numeric-method linearize,InteractionSet,GRanges-method linearize,InteractionSet,numeric-method |
| Link overlapping regions | linkOverlaps 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 ranges | makeGInteractionsFromGRangesPairs pairs pairs,GInteractions-method pairs,InteractionSet-method |
| Update a GInteractions object | updateObject updateObject,GInteractions-method |
