S4Vectors

DOI: 10.18129/B9.bioc.S4Vectors  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see S4Vectors.

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

Bioconductor version: 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>

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")

 

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

Details

biocViews	DataRepresentation, Infrastructure, Software
Version	0.38.2
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
LinkingTo
Suggests	IRanges, GenomicRanges, SummarizedExperiment, Matrix, DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle, knitr
SystemRequirements
Enhances
URL	https://bioconductor.org/packages/S4Vectors
BugReports	https://github.com/Bioconductor/S4Vectors/issues
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, BioMartGOGeneSets, 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, lefser, 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, MoleculeExperiment, 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_0.38.2.tar.gz
Windows Binary	S4Vectors_0.38.2.zip
macOS Binary (x86_64)	S4Vectors_0.38.2.tgz
macOS Binary (arm64)	S4Vectors_0.38.2.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