Package: SummarizedExperiment 1.41.1
Hervé Pagès
SummarizedExperiment: A container (S4 class) for matrix-like assays
The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.
Authors:
SummarizedExperiment_1.41.1.tar.gz
SummarizedExperiment_1.41.1.zip(r-4.6)SummarizedExperiment_1.41.1.zip(r-4.5)SummarizedExperiment_1.41.1.zip(r-4.4)
SummarizedExperiment_1.41.1.tgz(r-4.6-any)SummarizedExperiment_1.41.1.tgz(r-4.5-any)
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SummarizedExperiment.pdf |SummarizedExperiment.html✨
SummarizedExperiment/json (API)
NEWS
| # Install 'SummarizedExperiment' in R: |
| install.packages('SummarizedExperiment', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bioconductor/summarizedexperiment/issues
On BioConductor:SummarizedExperiment-1.41.0(bioc 3.23)SummarizedExperiment-1.40.0(bioc 3.22)
geneticsinfrastructuresequencingannotationcoveragegenomeannotationbioconductor-packagecore-package
Last updated from:66ad59a35d. Checks:1 WARNING, 6 NOTE, 3 OK. Indexed: yes.
| Target | Result | Total time | Artifact |
|---|---|---|---|
| bioc-checks | WARNING | 263 | |
| linux-devel-x86_64 | NOTE | 373 | |
| source / vignettes | OK | 328 | |
| linux-release-x86_64 | NOTE | 364 | |
| macos-devel-arm64 | NOTE | 353 | |
| macos-release-arm64 | NOTE | 273 | |
| windows-devel | NOTE | 306 | |
| windows-release | NOTE | 284 | |
| windows-oldrel | OK | 268 | |
| wasm-release | OK | 221 |
Exports:.DollarNames.RangedSummarizedExperiment.DollarNames.SummarizedExperimentacbindarbindas.data.frameassayassay<-assayNamesassayNames<-assaysAssaysassays<-cbindcoercecolDatacolData<-colnamescombineColscombineRowsComparecoveragedisjointBinsdistancedistanceToNearestduplicatedelementMetadataelementMetadata<-endend<-findOverlapsflankfollowgeneRangeMapperhorizontal_slot_namesis.unsortedisDisjointmakeSummarizedExperimentFromDataFramemakeSummarizedExperimentFromExpressionSetmakeSummarizedExperimentFromLoommatchmcolsmcols<-mergemetadata<-naiveRangeMappernarrowncolnearestnroworderparallel_slot_namespcompareprecedeprobeRangeMapperpromotersrangesranges<-rankrbindrealizeresizerestrictrowDatarowData<-rownamesrowRangesrowRanges<-saveRDSseqinfoseqinfo<-seqnamesseqnames<-shiftshowshowAsCellsortstartstart<-strandstrand<-subsetSummarizedExperimentterminatorstrimupdateObjectvaluesvalues<-vertical_slot_nameswidthwidth<-
Dependencies:abindBiobaseBiocGenericsDelayedArraygenericsGenomicRangesIRangeslatticeMatrixMatrixGenericsmatrixStatsS4ArraysS4VectorsSeqinfoSparseArrayXVector
SummarizedExperiment for Coordinating Experimental Assays, Samples, and Regions of Interest
Rendered fromSummarizedExperiment.Rmdusingknitr::rmarkdownon Feb 06 2026.Last update: 2024-01-05
Started: 2015-05-14
Extending the SummarizedExperiment class
Rendered fromExtensions.Rmdusingknitr::rmarkdownon Feb 06 2026.Last update: 2018-10-30
Started: 2018-05-03
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Assays objects | acbind,Matrix-method arbind,Matrix-method Assays Assays-class AssaysInEnv AssaysInEnv-class cbind,Assays-method class:Assays class:AssaysInEnv class:ShallowData class:ShallowSimpleListAssays class:SimpleAssays coerce,AssaysInEnv,SimpleList-method coerce,ShallowSimpleListAssays,SimpleList-method coerce,SimpleAssays,SimpleList-method coerce,SimpleList,AssaysInEnv-method coerce,SimpleList,ShallowSimpleListAssays-method coerce,SimpleList,SimpleAssays-method dim,Assays-method getListElement,Assays-method getListElement,AssaysInEnv-method length,Assays-method length,AssaysInEnv-method names,Assays-method names,AssaysInEnv-method names<-,Assays-method names<-,AssaysInEnv-method rbind,Assays-method setListElement,Assays-method setListElement,AssaysInEnv-method ShallowData ShallowData-class ShallowSimpleListAssays ShallowSimpleListAssays-class SimpleAssays SimpleAssays-class updateObject,Assays-method [,Assays,ANY,ANY,ANY-method [,Assays,ANY-method [<-,Assays,ANY,ANY,ANY-method |
| Coverage of a RangedSummarizedExperiment object | coverage coverage,RangedSummarizedExperiment-method coverage-methods |
| Finding overlapping ranges in RangedSummarizedExperiment objects | findOverlaps findOverlaps,RangedSummarizedExperiment,RangedSummarizedExperiment-method findOverlaps,RangedSummarizedExperiment,Vector-method findOverlaps,Vector,RangedSummarizedExperiment-method findOverlaps-methods |
| Inter range transformations of a RangedSummarizedExperiment object | disjointBins disjointBins,RangedSummarizedExperiment-method inter-range-methods isDisjoint isDisjoint,RangedSummarizedExperiment-method |
| Intra range transformations of a RangedSummarizedExperiment object | flank flank,RangedSummarizedExperiment-method intra-range-methods narrow narrow,RangedSummarizedExperiment-method promoters promoters,RangedSummarizedExperiment-method resize resize,RangedSummarizedExperiment-method restrict restrict,RangedSummarizedExperiment-method shift shift,RangedSummarizedExperiment-method terminators terminators,RangedSummarizedExperiment-method trim,RangedSummarizedExperiment-method |
| Make a RangedSummarizedExperiment from a data.frame or DataFrame | makeSummarizedExperimentFromDataFrame |
| Make a RangedSummarizedExperiment object from an ExpressionSet and vice-versa | coerce,ExpressionSet,RangedSummarizedExperiment-method coerce,ExpressionSet,SummarizedExperiment-method coerce,RangedSummarizedExperiment,ExpressionSet-method coerce,SummarizedExperiment,ExpressionSet-method geneRangeMapper makeSummarizedExperimentFromExpressionSet naiveRangeMapper probeRangeMapper |
| Make a SummarizedExperiment from a '.loom' hdf5 file | makeSummarizedExperimentFromLoom |
| Finding the nearest range neighbor in RangedSummarizedExperiment objects | distance distance,ANY,RangedSummarizedExperiment-method distance,RangedSummarizedExperiment,ANY-method distance,RangedSummarizedExperiment,RangedSummarizedExperiment-method distanceToNearest distanceToNearest,ANY,RangedSummarizedExperiment-method distanceToNearest,RangedSummarizedExperiment,ANY-method distanceToNearest,RangedSummarizedExperiment,RangedSummarizedExperiment-method follow follow,ANY,RangedSummarizedExperiment-method follow,RangedSummarizedExperiment,ANY-method follow,RangedSummarizedExperiment,RangedSummarizedExperiment-method nearest nearest,ANY,RangedSummarizedExperiment-method nearest,RangedSummarizedExperiment,ANY-method nearest,RangedSummarizedExperiment,RangedSummarizedExperiment-method nearest-methods precede precede,ANY,RangedSummarizedExperiment-method precede,RangedSummarizedExperiment,ANY-method precede,RangedSummarizedExperiment,RangedSummarizedExperiment-method |
| RangedSummarizedExperiment objects | class:RangedSummarizedExperiment coerce,RangedSummarizedExperiment,SummarizedExperiment-method coerce,SummarizedExperiment,RangedSummarizedExperiment-method Compare,ANY,RangedSummarizedExperiment-method Compare,RangedSummarizedExperiment,ANY-method Compare,RangedSummarizedExperiment,RangedSummarizedExperiment-method dimnames<-,RangedSummarizedExperiment,list-method duplicated,RangedSummarizedExperiment-method elementMetadata,RangedSummarizedExperiment-method elementMetadata<-,RangedSummarizedExperiment-method end,RangedSummarizedExperiment-method end<-,RangedSummarizedExperiment-method granges,RangedSummarizedExperiment-method is.unsorted,RangedSummarizedExperiment-method mcols,RangedSummarizedExperiment-method mcols<-,RangedSummarizedExperiment-method names,RangedSummarizedExperiment-method names<-,RangedSummarizedExperiment-method order,RangedSummarizedExperiment-method parallel_slot_names,RangedSummarizedExperiment-method pcompare,ANY,RangedSummarizedExperiment-method pcompare,RangedSummarizedExperiment,ANY-method pcompare,RangedSummarizedExperiment,RangedSummarizedExperiment-method RangedSummarizedExperiment RangedSummarizedExperiment-class ranges,RangedSummarizedExperiment-method ranges<-,RangedSummarizedExperiment-method rank,RangedSummarizedExperiment-method rowRanges rowRanges,RangedSummarizedExperiment-method rowRanges,SummarizedExperiment-method rowRanges<- rowRanges<-,RangedSummarizedExperiment,NULL-method rowRanges<-,SummarizedExperiment,GenomicRanges-method rowRanges<-,SummarizedExperiment,GRangesList-method rowRanges<-,SummarizedExperiment,NULL-method seqinfo,RangedSummarizedExperiment-method seqinfo<-,RangedSummarizedExperiment-method seqnames,RangedSummarizedExperiment-method sort,RangedSummarizedExperiment-method split,RangedSummarizedExperiment,ANY-method split,RangedSummarizedExperiment-method start,RangedSummarizedExperiment-method start<-,RangedSummarizedExperiment-method strand,RangedSummarizedExperiment-method strand<-,RangedSummarizedExperiment,ANY-method subset,RangedSummarizedExperiment-method updateObject,RangedSummarizedExperiment-method width,RangedSummarizedExperiment-method width<-,RangedSummarizedExperiment-method |
| SummarizedExperiment objects | $,SummarizedExperiment-method $<-,SummarizedExperiment-method assay assay,SummarizedExperiment,character-method assay,SummarizedExperiment,missing-method assay,SummarizedExperiment,numeric-method assay<- assay<-,SummarizedExperiment,character-method assay<-,SummarizedExperiment,missing-method assay<-,SummarizedExperiment,numeric-method assayNames assayNames,SummarizedExperiment-method assayNames<- assayNames<-,SummarizedExperiment,character-method assays assays,SummarizedExperiment-method assays<- assays<-,SummarizedExperiment,list-method assays<-,SummarizedExperiment,SimpleList-method Assays_OR_NULL Assays_OR_NULL-class cbind,SummarizedExperiment-method class:Assays_OR_NULL class:SummarizedExperiment colData colData,SummarizedExperiment-method colData<- colData<-,SummarizedExperiment,DataFrame-method colData<-,SummarizedExperiment,NULL-method colnames,SummarizedExperiment-method combineCols combineCols,SummarizedExperiment-method combineRows combineRows,SummarizedExperiment-method dimnames<-,SummarizedExperiment,list-method dimnames<-,SummarizedExperiment,NULL-method horizontal_slot_names,SummarizedExperiment-method length,SummarizedExperiment-method names,SummarizedExperiment-method names<-,SummarizedExperiment-method ncol,SummarizedExperiment-method nrow,SummarizedExperiment-method parallel_slot_names,SummarizedExperiment-method rbind,SummarizedExperiment-method realize,SummarizedExperiment-method rowData rowData,SummarizedExperiment-method rowData<- rowData<-,SummarizedExperiment-method rownames,SummarizedExperiment-method saveRDS,SummarizedExperiment-method show,SummarizedExperiment-method showAsCell,SummarizedExperiment-method subset,SummarizedExperiment-method SummarizedExperiment SummarizedExperiment-class updateObject,SummarizedExperiment-method vertical_slot_names,SummarizedExperiment-method [,SummarizedExperiment,ANY,ANY,ANY-method [,SummarizedExperiment,ANY-method [,SummarizedExperiment-method [<-,SummarizedExperiment,ANY,ANY,SummarizedExperiment-method [[,SummarizedExperiment,ANY,missing-method [[<-,SummarizedExperiment,ANY,missing-method |
