S4Vectors

This is the released version of S4Vectors; for the devel version, see S4Vectors.

Foundation of vector-like and list-like containers in Bioconductor

Bioconductor version: Release (3.21)

The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, Factor, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages).

Author: Hervé Pagès [aut, cre], Michael Lawrence [aut], Patrick Aboyoun [aut], Aaron Lun [ctb], Beryl Kanali [ctb] (Converted vignettes from Sweave to RMarkdown)

Maintainer: Hervé Pagès <hpages.on.github at gmail.com>

Citation (from within R, enter citation("S4Vectors")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("S4Vectors")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("S4Vectors")

A quick overview of the S4 class system	PDF	R Script
An Overview of the S4Vectors package	HTML	R Script
Rle Tips and Tricks	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataRepresentation, Infrastructure, Software
Version	0.46.0
In Bioconductor since	BioC 3.0 (R-3.1) (10.5 years)
License	Artistic-2.0
Depends	R (>= 4.0.0), methods, utils, stats, stats4, BiocGenerics(>= 0.53.2)
Imports
System Requirements
URL	https://bioconductor.org/packages/S4Vectors
Bug Reports	https://github.com/Bioconductor/S4Vectors/issues

Suggests	IRanges, GenomicRanges, SummarizedExperiment, Matrix, DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle, knitr
Linking To
Enhances
Depends On Me	altcdfenvs, AnnotationHubData, ATACseqQC, bambu, bandle, betaHMM, Biostrings, BiSeq, BSgenome, bumphunter, Cardinal, CellMapper, CexoR, chimeraviz, ChIPpeakAnno, chipseq, ChIPseqR, ClassifyR, cliProfiler, CODEX, CompoundDb, coseq, CSAR, CSSQ, DelayedArray, DelayedDataFrame, DESeq2, DEXSeq, DirichletMultinomial, DMCFB, DMCHMM, DMRcaller, epigenomix, ExperimentHubData, ExpressionAtlas, fCCAC, GA4GHclient, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, GenomicScores, GenomicTuples, GeomxTools, girafe, groHMM, Gviz, hdxmsqc, HelloRanges, HERON, InTAD, IntEREst, IRanges, LinTInd, LoomExperiment, m6Aboost, MetNet, MotifDb, MSnbase, MuData, MultimodalExperiment, NADfinder, NanoStringNCTools, NBAMSeq, octad, OGRE, OTUbase, padma, PSMatch, pwalign, Rcwl, RegEnrich, RepViz, RNAmodR, RnBeads, S4Arrays, scDataviz, screenCounter, segmentSeq, seqArchRplus, SeqGate, SparseArray, Spectra, SQLDataFrame, strandCheckR, Structstrings, topdownr, TreeSummarizedExperiment, TRESS, triplex, txdbmaker, updateObject, VariantExperiment, VariantTools, vulcan, XVector, pd.ag, pd.aragene.1.0.st, pd.aragene.1.1.st, pd.ath1.121501, pd.barley1, pd.bovgene.1.0.st, pd.bovgene.1.1.st, pd.bovine, pd.bsubtilis, pd.cangene.1.0.st, pd.cangene.1.1.st, pd.canine, pd.canine.2, pd.celegans, pd.chicken, pd.chigene.1.0.st, pd.chigene.1.1.st, pd.chogene.2.0.st, pd.chogene.2.1.st, pd.citrus, pd.clariom.d.human, pd.clariom.s.human, pd.clariom.s.human.ht, pd.clariom.s.mouse, pd.clariom.s.mouse.ht, pd.clariom.s.rat, pd.clariom.s.rat.ht, pd.cotton, pd.cyngene.1.0.st, pd.cyngene.1.1.st, pd.cyrgene.1.0.st, pd.cyrgene.1.1.st, pd.cytogenetics.array, pd.drogene.1.0.st, pd.drogene.1.1.st, pd.drosgenome1, pd.drosophila.2, pd.e.coli.2, pd.ecoli, pd.ecoli.asv2, pd.elegene.1.0.st, pd.elegene.1.1.st, pd.equgene.1.0.st, pd.equgene.1.1.st, pd.felgene.1.0.st, pd.felgene.1.1.st, pd.fingene.1.0.st, pd.fingene.1.1.st, pd.genomewidesnp.5, pd.genomewidesnp.6, pd.guigene.1.0.st, pd.guigene.1.1.st, pd.hc.g110, pd.hg.focus, pd.hg.u133.plus.2, pd.hg.u133a, pd.hg.u133a.2, pd.hg.u133a.tag, pd.hg.u133b, pd.hg.u219, pd.hg.u95a, pd.hg.u95av2, pd.hg.u95b, pd.hg.u95c, pd.hg.u95d, pd.hg.u95e, pd.hg18.60mer.expr, pd.ht.hg.u133.plus.pm, pd.ht.hg.u133a, pd.ht.mg.430a, pd.hta.2.0, pd.hu6800, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, pd.hugene.1.1.st.v1, pd.hugene.2.0.st, pd.hugene.2.1.st, pd.maize, pd.mapping250k.nsp, pd.mapping250k.sty, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.margene.1.0.st, pd.margene.1.1.st, pd.medgene.1.0.st, pd.medgene.1.1.st, pd.medicago, pd.mg.u74a, pd.mg.u74av2, pd.mg.u74b, pd.mg.u74bv2, pd.mg.u74c, pd.mg.u74cv2, pd.mirna.1.0, pd.mirna.2.0, pd.mirna.3.0, pd.mirna.4.0, pd.moe430a, pd.moe430b, pd.moex.1.0.st.v1, pd.mogene.1.0.st.v1, pd.mogene.1.1.st.v1, pd.mogene.2.0.st, pd.mogene.2.1.st, pd.mouse430.2, pd.mouse430a.2, pd.mta.1.0, pd.mu11ksuba, pd.mu11ksubb, pd.nugo.hs1a520180, pd.nugo.mm1a520177, pd.ovigene.1.0.st, pd.ovigene.1.1.st, pd.pae.g1a, pd.plasmodium.anopheles, pd.poplar, pd.porcine, pd.porgene.1.0.st, pd.porgene.1.1.st, pd.rabgene.1.0.st, pd.rabgene.1.1.st, pd.rae230a, pd.rae230b, pd.raex.1.0.st.v1, pd.ragene.1.0.st.v1, pd.ragene.1.1.st.v1, pd.ragene.2.0.st, pd.ragene.2.1.st, pd.rat230.2, pd.rcngene.1.0.st, pd.rcngene.1.1.st, pd.rg.u34a, pd.rg.u34b, pd.rg.u34c, pd.rhegene.1.0.st, pd.rhegene.1.1.st, pd.rhesus, pd.rice, pd.rjpgene.1.0.st, pd.rjpgene.1.1.st, pd.rn.u34, pd.rta.1.0, pd.rusgene.1.0.st, pd.rusgene.1.1.st, pd.s.aureus, pd.soybean, pd.soygene.1.0.st, pd.soygene.1.1.st, pd.sugar.cane, pd.tomato, pd.u133.x3p, pd.vitis.vinifera, pd.wheat, pd.x.laevis.2, pd.x.tropicalis, pd.xenopus.laevis, pd.yeast.2, pd.yg.s98, pd.zebgene.1.0.st, pd.zebgene.1.1.st, pd.zebrafish, curatedPCaData, scATAC.Explorer, generegulation
Imports Me	ADImpute, adverSCarial, affycoretools, aggregateBioVar, airpart, alabaster.base, alabaster.bumpy, alabaster.files, alabaster.mae, alabaster.matrix, alabaster.ranges, alabaster.se, alabaster.sfe, alabaster.spatial, alabaster.string, alabaster.vcf, ALDEx2, AllelicImbalance, amplican, AneuFinder, animalcules, AnnotationDbi, AnnotationForge, AnnotationHub, annotatr, appreci8R, ASpli, ASURAT, ATACseqTFEA, atena, autonomics, BadRegionFinder, ballgown, Banksy, barbieQ, barcodetrackR, BASiCS, batchelor, BatchQC, BayesSpace, bettr, BindingSiteFinder, BiocHubsShiny, BiocIO, BiocSet, BiocSingular, biotmle, biovizBase, biscuiteer, BiSeq, bluster, bnbc, BPRMeth, branchpointer, breakpointR, BREW3R.r, BSgenomeForge, bsseq, BumpyMatrix, BUSpaRse, BUSseq, CAGEfightR, CAGEr, cardelino, CardinalIO, CARDspa, casper, CATALYST, CatsCradle, cBioPortalData, ccfindR, celaref, celda, CellBarcode, censcyt, Cepo, CeTF, cfdnakit, CHETAH, chevreulPlot, chevreulProcess, chevreulShiny, chipenrich, ChIPexoQual, ChIPQC, ChIPseeker, ChromSCape, chromVAR, cicero, circRNAprofiler, CircSeqAlignTk, CiteFuse, cleanUpdTSeq, cleaver, CluMSID, clusterExperiment, clustifyr, cn.mops, CNEr, CNVMetrics, CNVPanelizer, CNVRanger, COCOA, CoGAPS, Cogito, comapr, compEpiTools, consensusDE, consensusSeekeR, CoreGx, COTAN, CoverageView, crisprBase, crisprDesign, CRISPRseek, crisprShiny, CrispRVariants, crisprViz, crupR, csaw, CTDquerier, cummeRbund, CuratedAtlasQueryR, customProDB, cydar, cytofQC, cytoKernel, cytomapper, cytoviewer, DAMEfinder, dandelionR, debrowser, DECIPHER, decompTumor2Sig, decontX, DeconvoBuddies, deconvR, DEFormats, DegCre, DegNorm, DEGreport, DelayedMatrixStats, derfinder, derfinderHelper, derfinderPlot, DEScan2, DESpace, DEWSeq, DFplyr, DiffBind, diffcyt, diffHic, diffUTR, Dino, DiscoRhythm, dittoSeq, DMRcate, dmrseq, DNAfusion, doseR, dreamlet, DRIMSeq, DropletUtils, drugTargetInteractions, dStruct, easyRNASeq, eisaR, ELMER, enhancerHomologSearch, EnrichDO, EnrichmentBrowser, ensembldb, epigraHMM, EpiMix, epimutacions, epiregulon, epistack, EpiTxDb, epivizr, epivizrData, epivizrStandalone, erma, esATAC, EventPointer, ExperimentHub, ExperimentSubset, ExploreModelMatrix, extraChIPs, factR, FastqCleaner, fastseg, FilterFFPE, FindIT2, fishpond, FLAMES, flowCore, flowWorkspace, FRASER, FuseSOM, G4SNVHunter, GA4GHshiny, gcapc, gDNAx, gDRcore, gDRimport, gDRutils, GDSArray, gemma.R, GeneRegionScan, GENESIS, GeneTonic, genomation, GenomAutomorphism, genomeIntervals, GenomicAlignments, GenomicFiles, GenomicInteractionNodes, GenomicInteractions, GenomicOZone, GenomicSuperSignature, geomeTriD, GEOquery, ggbio, Glimma, glmGamPoi, gmapR, gmoviz, GOpro, GOTHiC, GRaNIE, GRmetrics, GSEABenchmarkeR, GSVA, GUIDEseq, gwascat, h5mread, h5vc, HDF5Array, hermes, HicAggR, HiCBricks, HiCcompare, HiCDOC, HiCExperiment, HiContacts, HiCool, HiCParser, hicVennDiagram, HiLDA, hipathia, hmdbQuery, HoloFoodR, icetea, ideal, IFAA, ILoReg, IMAS, imcRtools, INSPEcT, InteractionSet, InteractiveComplexHeatmap, iSEE, iSEEde, iSEEhub, iSEEpathways, iSEEtree, iSEEu, IsoBayes, IsoformSwitchAnalyzeR, isomiRs, IVAS, ivygapSE, karyoploteR, katdetectr, kebabs, kmcut, knowYourCG, lefser, lemur, limpca, LimROTS, lionessR, lipidr, lisaClust, loci2path, LOLA, lute, MACSr, MADSEQ, magpie, MAI, mariner, marr, MAST, mbkmeans, mCSEA, MEAL, meshr, MesKit, metabCombiner, MetaboAnnotation, MetaboDynamics, metaseqR2, MetCirc, methInheritSim, methodical, MethReg, methrix, methylCC, methylInheritance, methylKit, methylPipe, methylSig, methylumi, MGnifyR, mia, miaDash, miaSim, miaViz, MICSQTL, midasHLA, miloR, mimager, minfi, MinimumDistance, MIRA, MiRaGE, missMethyl, missRows, mist, mitoClone2, MMDiff2, moanin, mobileRNA, Modstrings, MoleculeExperiment, monaLisa, mosaics, MOSClip, mosdef, MOSim, Motif2Site, motifbreakR, motifmatchr, MotifPeeker, motifTestR, MPAC, mpra, msa, MsBackendMassbank, MsBackendMetaboLights, MsBackendMgf, MsBackendMsp, MsBackendRawFileReader, MsBackendSql, MsCoreUtils, MsExperiment, msgbsR, MSPrep, MuData, MultiAssayExperiment, MultiDataSet, MultiRNAflow, multistateQTL, mumosa, muscat, musicatk, MutationalPatterns, mygene, myvariant, NanoMethViz, ncRNAtools, nearBynding, nucleoSim, nucleR, nullranges, oligoClasses, omicsViewer, oncoscanR, ontoProc, openPrimeR, ORFik, Organism.dplyr, OrganismDbi, orthos, OUTRIDER, OutSplice, packFinder, PAIRADISE, pairedGSEA, panelcn.mops, PAST, pcaExplorer, PDATK, pdInfoBuilder, Pedixplorer, periodicDNA, pgxRpi, PharmacoGx, PhIPData, PhosR, PICB, PING, pipeComp, Pirat, plyinteractions, plyranges, plyxp, pmp, pogos, PolySTest, pqsfinder, pram, prebs, preciseTAD, primirTSS, proActiv, procoil, proDA, profileplyr, PRONE, ProteoDisco, PureCN, PWMEnrich, qcmetrics, QFeatures, qpgraph, qsea, QTLExperiment, QuasR, R3CPET, R453Plus1Toolbox, RadioGx, raer, RaggedExperiment, RAIDS, ramr, RareVariantVis, RBioFormats, RCAS, RcisTarget, RcwlPipelines, recount, recount3, recountmethylation, recoup, ReducedExperiment, RegionalST, regioneR, regionReport, regsplice, regutools, REMP, Repitools, ResidualMatrix, RESOLVE, ReUseData, rexposome, rfaRm, RFLOMICS, RgnTX, rGREAT, RiboDiPA, RiboProfiling, ribor, riboSeqR, ribosomeProfilingQC, rifi, rifiComparative, RJMCMCNucleosomes, RMassBank, Rmmquant, rnaEditr, RNAmodR.AlkAnilineSeq, RNAmodR.ML, RNAmodR.RiboMethSeq, roar, rprimer, Rqc, Rsamtools, rScudo, RTCGAToolbox, RTN, rtracklayer, RUCova, saseR, SC3, ScaledMatrix, scanMiR, scanMiRApp, SCArray, SCArray.sat, scater, scClassify, scDblFinder, scDD, scds, scHOT, scider, scmap, scMerge, scMET, SCnorm, SCOPE, scp, scPipe, scran, scRepertoire, scRNAseqApp, scruff, scTensor, scTGIF, scTreeViz, scuttle, scviR, sechm, segmenter, SeqArray, seqCAT, seqsetvis, SeqSQC, SeqVarTools, sesame, SEtools, sevenbridges, sevenC, SGSeq, shinyDSP, ShortRead, simona, simPIC, simpleSeg, SingleCellAlleleExperiment, SingleCellExperiment, singleCellTK, SingleMoleculeFootprinting, SingleR, singscore, sitadela, Site2Target, skewr, slingshot, SMITE, SNPhood, soGGi, SomaticSignatures, SOMNiBUS, sosta, Spaniel, SpaNorm, SpatialExperiment, SpatialExperimentIO, SpatialFeatureExperiment, spatialHeatmap, SpatialOmicsOverlay, spatzie, spicyR, spiky, spillR, splatter, SpliceWiz, SplicingGraphs, SplineDV, SPLINTER, SpotClean, sRACIPE, srnadiff, standR, Statial, struct, StructuralVariantAnnotation, SummarizedExperiment, svaNUMT, svaRetro, SVP, SynExtend, systemPipeR, tadar, TAPseq, TBSignatureProfiler, TCGAbiolinks, TCGAutils, TENET, TENxIO, terraTCGAdata, TFBSTools, TFHAZ, tidybulk, tidyCoverage, tidySingleCellExperiment, tidySpatialExperiment, tidySummarizedExperiment, TileDBArray, TnT, ToxicoGx, trackViewer, tradeSeq, TrajectoryUtils, transcriptR, transmogR, treeclimbR, Trendy, tricycle, tRNA, tRNAdbImport, tRNAscanImport, TSCAN, TVTB, twoddpcr, txcutr, tximeta, UCSC.utils, Ularcirc, UMI4Cats, universalmotif, UPDhmm, VanillaICE, VariantAnnotation, VariantFiltering, VaSP, VCFArray, VDJdive, velociraptor, VisiumIO, visiumStitched, Voyager, VplotR, wavClusteR, weitrix, wiggleplotr, xcms, xcore, XeniumIO, xenLite, XNAString, XVector, yamss, zellkonverter, BioMartGOGeneSets, fitCons.UCSC.hg19, MafDb.1Kgenomes.phase1.GRCh38, MafDb.1Kgenomes.phase1.hs37d5, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ExAC.r1.0.GRCh38, MafDb.ExAC.r1.0.hs37d5, MafDb.ExAC.r1.0.nonTCGA.GRCh38, MafDb.ExAC.r1.0.nonTCGA.hs37d5, MafDb.gnomAD.r2.1.GRCh38, MafDb.gnomAD.r2.1.hs37d5, MafDb.gnomADex.r2.1.GRCh38, MafDb.gnomADex.r2.1.hs37d5, MafDb.TOPMed.freeze5.hg19, MafDb.TOPMed.freeze5.hg38, MafH5.gnomAD.v4.0.GRCh38, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, bugphyzz, celldex, chipenrich.data, chipseqDBData, curatedMetagenomicData, curatedTCGAData, DNAZooData, DropletTestFiles, FlowSorted.Blood.EPIC, fourDNData, HCATonsilData, HighlyReplicatedRNASeq, HMP16SData, HMP2Data, homosapienDEE2CellScore, imcdatasets, leeBamViews, LegATo, MerfishData, MetaGxPancreas, MetaScope, MethylSeqData, MicrobiomeBenchmarkData, MouseGastrulationData, MouseThymusAgeing, pd.atdschip.tiling, scMultiome, scpdata, scRNAseq, sesameData, SimBenchData, SingleCellMultiModal, SomaticCancerAlterations, spatialLIBD, TransOmicsData, tuberculosis, GeoMxWorkflows, crispRdesignR, DR.SC, driveR, genBaRcode, geno2proteo, hoardeR, imcExperiment, karyotapR, LoopRig, MetAlyzer, microbial, multimedia, NIPTeR, oncoPredict, PlasmaMutationDetector, restfulr, rliger, rnaCrosslinkOO, rsolr, SC.MEB, SCRIP, scROSHI, Signac, SpatialDDLS, TaxaNorm, toxpiR
Suggests Me	AlpsNMR, ANCOMBC, BiocGenerics, CCAFE, chihaya, dearseq, epiregulon.extra, epivizrChart, GeoTcgaData, globalSeq, GWASTools, GWENA, gypsum, hca, koinar, maftools, martini, MicrobiotaProcess, MsQuality, MungeSumstats, RTCGA, scFeatures, scrapper, SpectraQL, SPOTlight, TFEA.ChIP, TFutils, XAItest, alternativeSplicingEvents.hg19, alternativeSplicingEvents.hg38, BioPlex, curatedAdipoChIP, curatedAdipoRNA, ObMiTi, xcoredata, gkmSVM, grandR, LorMe, MARVEL, pmartR, polyRAD, pQTLdata, RCPA, Rgff, Seurat, SNPassoc, updog, valr
Links To Me	Biostrings, CNEr, DECIPHER, DelayedArray, GenomicAlignments, GenomicRanges, h5mread, IRanges, kebabs, MatrixRider, pwalign, Rsamtools, rtracklayer, S4Arrays, ShortRead, SparseArray, Structstrings, triplex, VariantAnnotation, VariantFiltering, XVector
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	S4Vectors_0.46.0.tar.gz
Windows Binary (x86_64)	S4Vectors_0.46.0.zip
macOS Binary (x86_64)	S4Vectors_0.46.0.tgz
macOS Binary (arm64)	S4Vectors_0.46.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/S4Vectors
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/S4Vectors
Bioc Package Browser	https://code.bioconductor.org/browse/S4Vectors/
Package Short Url	https://bioconductor.org/packages/S4Vectors/
Package Downloads Report	Download Stats