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, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages).
Author: H. Pagès, M. Lawrence and P. Aboyoun
To view documentation for the version of this package installed
in your system, start R and enter:
| biocViews |
DataRepresentation, Infrastructure, Software |
| Version |
0.16.0 |
| In Bioconductor since |
BioC 3.0 (R-3.1) (3.5 years) |
| License |
Artistic-2.0 |
| Depends |
R (>= 3.3.0), methods, utils, stats, stats4, BiocGenerics(>= 0.23.3) |
| Imports |
|
| LinkingTo |
|
| Suggests |
IRanges, GenomicRanges, Matrix, ShortRead, graph, data.table, RUnit |
| SystemRequirements |
|
| Enhances |
|
| URL |
|
| Depends On Me |
altcdfenvs, AnnotationHubData, ATACseqQC, Biostrings, BiSeq, BSgenome, bumphunter, CellMapper, CexoR, chimeraviz, ChIPComp, ChIPpeakAnno, chipseq, ChIPseqR, CODEX, coseq, CSAR, DelayedArray, DESeq2, DEXSeq, DirichletMultinomial, DMCHMM, DMRcaller, epigenomix, ExperimentHubData, ExpressionAtlas, fCCAC, GA4GHclient, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, GenomicScores, GenomicTuples, girafe, groHMM, Gviz, HelloRanges, htSeqTools, InPAS, IntEREst, IRanges, meshr, MotifDb, NADfinder, OTUbase, 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, RIPSeeker, RnBeads, segmentSeq, SNPlocs.Hsapiens.dbSNP141.GRCh38, topdownr, triplex, VariantTools, vulcan, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, XVector |
| Imports Me |
affycoretools, ALDEx2, AllelicImbalance, alpine, amplican, anamiR, AneuFinder, AnnotationDbi, AnnotationForge, AnnotationHub, annotatr, ArrayTV, ASpli, BadRegionFinder, ballgown, BASiCS, BasicSTARRseq, biovizBase, BiSeq, BitSeq, bnbc, BPRMeth, branchpointer, BSgenome, bsseq, casper, cgdv17, ChIPanalyser, chipenrich, chipenrich.data, ChIPexoQual, ChIPQC, ChIPseeker, chromstaR, chromswitch, chromVAR, CINdex, cleaver, cn.mops, CNEr, CNPBayes, CNVPanelizer, coMET, compEpiTools, consensusSeekeR, contiBAIT, copynumber, CopywriteR, CoverageView, CRISPRseek, CrispRVariants, csaw, cummeRbund, curatedMetagenomicData, curatedTCGAData, customProDB, cydar, DChIPRep, debrowser, DECIPHER, DEGreport, DelayedMatrixStats, derfinder, derfinderHelper, derfinderPlot, DiffBind, diffHic, diffloop, DMRcate, DOSE, DRIMSeq, easyRNASeq, eegc, ELMER, EnrichmentBrowser, ensembldb, ensemblVEP, epivizr, epivizrData, epivizrStandalone, erma, esATAC, EventPointer, ExperimentHub, facopy, fastseg, FindMyFriends, fitCons.UCSC.hg19, FunciSNP, GA4GHshiny, gcapc, genbankr, genefilter, GeneRegionScan, GENESIS, GenoGAM, genomation, genomeIntervals, GenomicAlignments, GenomicFiles, GenomicInteractions, genoset, GGBase, ggbio, GGtools, Glimma, gmapR, GoogleGenomics, GOpro, GOTHiC, gQTLBase, gQTLstats, GRmetrics, GUIDEseq, gwascat, h5vc, HDF5Array, HiCcompare, HTSeqGenie, ideal, IMAS, ImpulseDE2, INSPEcT, InteractionSet, InterMineR, isomiRs, IVAS, ivygapSE, IWTomics, JunctionSeq, karyoploteR, kebabs, LOLA, M3D, MADSEQ, MafDb.1Kgenomes.phase1.hs37d5, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ESP6500SI.V2.SSA137.GRCh38, MafDb.ESP6500SI.V2.SSA137.hs37d5, MafDb.ExAC.r1.0.hs37d5, MafDb.ExAC.r1.0.nonTCGA.hs37d5, MafDb.gnomAD.r2.0.1.hs37d5, MafDb.gnomADex.r2.0.1.hs37d5, MafDb.TOPMed.freeze5.hg38, MAST, MEAL, methInheritSim, methylInheritance, methylKit, methylPipe, methylumi, mimager, minfi, MinimumDistance, MIRA, MiRaGE, MMDiff2, mosaics, motifbreakR, motifmatchr, MotIV, mpra, msa, msgbsR, MSnbase, MultiAssayExperiment, MultiDataSet, MutationalPatterns, mygene, myvariant, NarrowPeaks, nucleoSim, nucleR, oligoClasses, ontoProc, openPrimeR, Organism.dplyr, OrganismDbi, panelcn.mops, PathwaySplice, Pbase, pcaExplorer, pd.atdschip.tiling, pdInfoBuilder, PGA, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, PICS, PING, polyester, pqsfinder, prebs, procoil, PureCN, qcmetrics, qpgraph, QuasR, R3CPET, R453Plus1Toolbox, RaggedExperiment, RareVariantVis, Rariant, Rcade, RCAS, recount, regioneR, regionReport, regsplice, REMP, Repitools, restfulSE, rexposome, rhdf5client, RiboProfiling, RJMCMCNucleosomes, RMassBank, RNAprobR, roar, Rqc, Rsamtools, RTCGAToolbox, RTN, rtracklayer, SC3, scater, scDD, scmap, SCnorm, scPipe, scran, SeqArray, seqCAT, seqplots, SeqSQC, SeqVarTools, sevenbridges, SGSeq, ShortRead, simulatorZ, SingleCellExperiment, SMITE, SNPchip, SNPhood, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, soGGi, SomaticCancerAlterations, SomaticSignatures, SplicingGraphs, SPLINTER, STAN, SummarizedExperiment, TarSeqQC, TCGAbiolinks, TFBSTools, TFHAZ, TnT, trackViewer, transcriptR, TransView, TSRchitect, TSSi, TVTB, twoddpcr, VanillaICE, VariantAnnotation, VariantFiltering, wavClusteR, wiggleplotr, xcms, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, XVector, yamss |
| Suggests Me |
alternativeSplicingEvents.hg19, BiocGenerics, epivizrChart, GWASTools, RTCGA, splatter |
| Build Report |
|
