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S4Vectors

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

Bioconductor version: Release (3.17)

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 'RleTricks' vignette 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 "4.3") 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 PDF R Script
Rle Tips and Tricks HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataRepresentation, Infrastructure, Software
Version 0.38.1
In Bioconductor since BioC 3.0 (R-3.1) (9 years)
License Artistic-2.0
Depends R (>= 4.0.0), methods, utils, stats, stats4, BiocGenerics(>= 0.37.0)
Imports
Linking To
Suggests IRanges, GenomicRanges, SummarizedExperiment, Matrix, DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle, knitr
System Requirements
Enhances
URL https://bioconductor.org/packages/S4Vectors
Bug Reports https://github.com/Bioconductor/S4Vectors/issues
See More
Depends On Me altcdfenvs, AnnotationHubData, ATACseqQC, bambu, bandle, Biostrings, BiSeq, BRGenomics, BSgenome, BSgenomeForge, bumphunter, Cardinal, CellMapper, CexoR, chimeraviz, ChIPComp, ChIPpeakAnno, chipseq, ChIPseqR, ClassifyR, cliProfiler, CODEX, CompoundDb, coseq, CSAR, CSSQ, DelayedArray, DelayedDataFrame, DESeq2, DEXSeq, DirichletMultinomial, DMCFB, DMCHMM, DMRcaller, epigenomix, epihet, ExperimentHubData, ExpressionAtlas, fCCAC, GA4GHclient, generegulation, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, GenomicScores, GenomicTuples, GeomxTools, girafe, groHMM, Gviz, HelloRanges, InTAD, IntEREst, IRanges, LinTInd, LoomExperiment, m6Aboost, MetNet, MotifDb, MSnbase, MuData, MultimodalExperiment, NADfinder, NanoStringNCTools, NBAMSeq, octad, OGRE, OTUbase, padma, 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, plethy, PSMatch, Rcwl, RegEnrich, RepViz, RNAmodR, RnBeads, S4Arrays, scATAC.Explorer, scDataviz, screenCounter, segmentSeq, seqArchRplus, SeqGate, SparseArray, Spectra, SQLDataFrame, Structstrings, SummarizedBenchmark, topdownr, TreeSummarizedExperiment, TRESS, triplex, updateObject, VariantExperiment, VariantTools, vulcan, XVector
Imports Me ADImpute, affycoretools, aggregateBioVar, airpart, alabaster.base, alabaster.bumpy, alabaster.mae, alabaster.ranges, alabaster.se, alabaster.spatial, alabaster.vcf, ALDEx2, AllelicImbalance, alpine, amplican, ANCOMBC, AneuFinder, animalcules, AnnotationDbi, AnnotationForge, AnnotationHub, annotatr, appreci8R, ASpediaFI, ASpli, ASURAT, ATACseqTFEA, atena, autonomics, BadRegionFinder, ballgown, barcodetrackR, BASiCS, BasicSTARRseq, batchelor, BayesSpace, BindingSiteFinder, BiocHubsShiny, BiocIO, BiocNeighbors, BiocOncoTK, BiocSet, BiocSingular, biotmle, biovizBase, biscuiteer, BiSeq, bluster, bnbc, BPRMeth, branchpointer, breakpointR, BSgenome, bsseq, BumpyMatrix, BUSpaRse, BUSseq, CAGEfightR, CAGEr, cardelino, casper, CATALYST, cBioPortalData, ccfindR, celaref, celda, CellaRepertorium, CellBarcode, celldex, censcyt, Cepo, CeTF, CHETAH, ChIC, ChIPanalyser, chipenrich, chipenrich.data, ChIPexoQual, ChIPQC, ChIPseeker, chipseqDBData, ChromSCape, chromstaR, chromswitch, chromVAR, cicero, CINdex, circRNAprofiler, CircSeqAlignTk, CiteFuse, cleanUpdTSeq, cleaver, CluMSID, clusterExperiment, clustifyr, cn.mops, CNEr, CNVMetrics, CNVPanelizer, CNVRanger, COCOA, CoGAPS, Cogito, comapr, coMET, compEpiTools, consensusDE, consensusSeekeR, contiBAIT, copynumber, CopywriteR, CoreGx, CoverageView, crisprBase, crisprDesign, CRISPRseek, CrispRVariants, crisprViz, csaw, CTDquerier, cummeRbund, curatedMetagenomicData, curatedTCGAData, customProDB, cydar, cytofQC, cytoKernel, cytomapper, cytoviewer, DAMEfinder, dasper, debrowser, DECIPHER, decompTumor2Sig, deconvR, DEFormats, DegNorm, DEGreport, DelayedMatrixStats, derfinder, derfinderHelper, derfinderPlot, DEScan2, DESpace, DEWSeq, DiffBind, diffcyt, diffHic, diffUTR, Dino, DiscoRhythm, dittoSeq, DMRcate, dmrseq, DNAfusion, DNAZooData, doseR, DRIMSeq, DropletTestFiles, DropletUtils, drugTargetInteractions, dStruct, easyRNASeq, eegc, eisaR, ELMER, enhancerHomologSearch, ENmix, EnrichmentBrowser, enrichTF, ensembldb, ensemblVEP, epigraHMM, EpiMix, epimutacions, epistack, EpiTxDb, epivizr, epivizrData, epivizrStandalone, erma, esATAC, EventPointer, exomePeak2, ExperimentHub, ExperimentSubset, ExploreModelMatrix, extraChIPs, factR, FastqCleaner, fastseg, FilterFFPE, FindIT2, fishpond, fitCons.UCSC.hg19, FLAMES, flowCore, FlowSorted.Blood.EPIC, flowWorkspace, fourDNData, FRASER, FuseSOM, GA4GHshiny, gcapc, GDSArray, gemma.R, genbankr, GeneRegionScan, GENESIS, GeneStructureTools, GeneTonic, genomation, GenomAutomorphism, genomeIntervals, GenomicAlignments, GenomicFiles, GenomicInteractionNodes, GenomicInteractions, GenomicOZone, GenomicSuperSignature, GeoMxWorkflows, ggbio, Glimma, gmapR, gmoviz, GOpro, GOTHiC, GRaNIE, GRmetrics, GSEABenchmarkeR, GSVA, GUIDEseq, gwascat, h5vc, HDF5Array, hermes, HiCBricks, HiCcompare, HiCDCPlus, HiCDOC, HiCExperiment, HiContacts, HiCool, HighlyReplicatedRNASeq, HiLDA, hipathia, hmdbQuery, HMP16SData, HMP2Data, HTSeqGenie, HumanTranscriptomeCompendium, icetea, ideal, IFAA, ILoReg, IMAS, imcdatasets, imcRtools, InPAS, INSPEcT, InteractionSet, InteractiveComplexHeatmap, InterMineR, iSEE, iSEEhub, iSEEu, IsoformSwitchAnalyzeR, isomiRs, IVAS, ivygapSE, IWTomics, karyoploteR, katdetectr, kebabs, leeBamViews, lionessR, lipidr, lisaClust, loci2path, LOLA, MACSr, MADSEQ, 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.v3.1.1.GRCh38, MafH5.gnomAD.v3.1.2.GRCh38, magpie, MAI, mariner, marr, MAST, mbkmeans, mCSEA, MEAL, MerfishData, meshr, MesKit, metabCombiner, MetaboAnnotation, MetaGxPancreas, MetaScope, metaseqR2, MetCirc, MethCP, methInheritSim, MethReg, methylCC, methylInheritance, methylKit, methylPipe, MethylSeqData, methylSig, methylumi, mia, miaSim, miaViz, MicrobiomeBenchmarkData, microbiomeMarker, midasHLA, miloR, mimager, minfi, MinimumDistance, MIRA, MiRaGE, missMethyl, missRows, mitoClone2, MMAPPR2, MMDiff2, moanin, Modstrings, monaLisa, mosaics, MOSim, Motif2Site, motifbreakR, motifmatchr, MouseGastrulationData, MouseThymusAgeing, mpra, msa, MsBackendMassbank, MsBackendMgf, MsBackendMsp, MsBackendRawFileReader, MsBackendSql, MsCoreUtils, MsExperiment, msgbsR, MSPrep, MultiAssayExperiment, MultiDataSet, mumosa, muscat, musicatk, MutationalPatterns, mygene, myvariant, NanoMethViz, ncRNAtools, nearBynding, netDx, NoRCE, nucleoSim, nucleR, nullranges, NxtIRFcore, ODER, oligoClasses, omicsViewer, oncoscanR, ontoProc, openPrimeR, ORFik, Organism.dplyr, OrganismDbi, OUTRIDER, OutSplice, packFinder, PAIRADISE, pairedGSEA, panelcn.mops, PAST, pcaExplorer, pd.atdschip.tiling, PDATK, pdInfoBuilder, periodicDNA, PharmacoGx, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, phemd, PhIPData, PhosR, PING, pipeComp, plyranges, pmp, pogos, polyester, pqsfinder, pram, prebs, preciseTAD, PrecisionTrialDrawer, primirTSS, proActiv, procoil, proDA, profileplyr, ProteoDisco, pulsedSilac, PureCN, PWMEnrich, qcmetrics, QFeatures, qpgraph, qsea, QuasR, R3CPET, R453Plus1Toolbox, RadioGx, RaggedExperiment, ramr, RareVariantVis, RBioFormats, RCAS, RcisTarget, RcwlPipelines, recount, recount3, recountmethylation, recoup, regioneR, regionReport, regsplice, regutools, REMP, Repitools, ResidualMatrix, RESOLVE, restfulSE, ReUseData, rexposome, rfaRm, RGMQL, RgnTX, rGREAT, RiboDiPA, RiboProfiling, ribor, ribosomeProfilingQC, rifi, rifiComparative, RJMCMCNucleosomes, RMassBank, Rmmquant, rnaEditr, RNAmodR.AlkAnilineSeq, RNAmodR.ML, RNAmodR.RiboMethSeq, roar, rprimer, Rqc, Rsamtools, rScudo, RTCGAToolbox, RTN, rtracklayer, SC3, ScaledMatrix, scanMiR, scanMiRApp, SCArray, SCArray.sat, scater, scClassify, scDblFinder, scDD, scds, scHOT, scmap, scMerge, scMET, scMultiome, SCnorm, SCOPE, scp, scpdata, scPipe, scran, scRNAseq, scRNAseqApp, scruff, scTensor, scTGIF, scTreeViz, scuttle, scviR, sechm, segmenter, SeqArray, seqCAT, seqpac, seqsetvis, SeqSQC, SeqVarTools, sesame, sesameData, SEtools, sevenbridges, sevenC, SGSeq, ShortRead, SimBenchData, simpleSeg, SingleCellExperiment, SingleCellMultiModal, singleCellTK, SingleR, singscore, sitadela, skewr, slingshot, SMITE, SNPhood, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, soGGi, SomaticCancerAlterations, SomaticSignatures, Spaniel, SpatialExperiment, SpatialFeatureExperiment, spatialHeatmap, spatialLIBD, SpatialOmicsOverlay, spatzie, spicyR, spiky, splatter, SpliceWiz, SplicingGraphs, SPLINTER, SpotClean, sRACIPE, srnadiff, STAN, standR, Statial, strandCheckR, struct, StructuralVariantAnnotation, SummarizedExperiment, svaNUMT, svaRetro, SynExtend, systemPipeR, TAPseq, TarSeqQC, TBSignatureProfiler, TCGAbiolinks, TCGAutils, TENxIO, terraTCGAdata, TFBSTools, TFHAZ, tidybulk, tidySingleCellExperiment, tidySummarizedExperiment, TileDBArray, TnT, ToxicoGx, trackViewer, tradeSeq, TrajectoryUtils, transcriptR, TransView, Trendy, tricycle, tRNA, tRNAdbImport, tRNAscanImport, TSCAN, tscR, tuberculosis, TVTB, twoddpcr, txcutr, tximeta, Ularcirc, UMI4Cats, uncoverappLib, universalmotif, VanillaICE, VariantAnnotation, VariantFiltering, VaSP, VCFArray, VDJdive, velociraptor, Voyager, VplotR, wavClusteR, weitrix, wiggleplotr, xcms, xcore, XNAString, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, XVector, yamss, zellkonverter
Suggests Me alabaster.matrix, AlpsNMR, alternativeSplicingEvents.hg19, alternativeSplicingEvents.hg38, BiocGenerics, BioPlex, chihaya, curatedAdipoChIP, curatedAdipoRNA, dearseq, epivizrChart, GeoTcgaData, globalSeq, GWASTools, GWENA, hca, maftools, martini, MicrobiotaProcess, MsQuality, MungeSumstats, ObMiTi, RTCGA, scFeatures, SPOTlight, TFEA.ChIP, TFutils, traviz, xcoredata
Links To Me Biostrings, CNEr, DECIPHER, DegNorm, DelayedArray, GenomicAlignments, GenomicRanges, HDF5Array, IRanges, kebabs, MatrixRider, Rsamtools, rtracklayer, S4Arrays, ShortRead, SparseArray, Structstrings, triplex, VariantAnnotation, VariantFiltering, XVector
Build Report  

Package Archives

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

Source Package S4Vectors_0.38.1.tar.gz
Windows Binary S4Vectors_0.38.1.zip
macOS Binary (x86_64) S4Vectors_0.38.1.tgz
macOS Binary (arm64) S4Vectors_0.38.1.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
Old Source Packages for BioC 3.17 Source Archive