Package: SummarizedExperiment 1.37.0

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:Martin Morgan [aut], Valerie Obenchain [aut], Jim Hester [aut], Hervé Pagès [aut, cre]

SummarizedExperiment_1.37.0.tar.gz
SummarizedExperiment_1.37.0.zip(r-4.5)SummarizedExperiment_1.37.0.zip(r-4.4)SummarizedExperiment_1.37.0.zip(r-4.3)
SummarizedExperiment_1.37.0.tgz(r-4.4-any)SummarizedExperiment_1.37.0.tgz(r-4.3-any)
SummarizedExperiment_1.37.0.tar.gz(r-4.5-noble)SummarizedExperiment_1.37.0.tar.gz(r-4.4-noble)
SummarizedExperiment_1.37.0.tgz(r-4.4-emscripten)SummarizedExperiment_1.37.0.tgz(r-4.3-emscripten)
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-1.37.0(bioc 3.21)SummarizedExperiment-1.36.0(bioc 3.20)

geneticsinfrastructuresequencingannotationcoveragegenomeannotationbioconductor-packagecore-package

16.92 score 34 stars 1.2k packages 8.6k scripts 85k downloads 52 mentions 88 exports 27 dependencies

Last updated 4 months agofrom:cbdaaaadf2. Checks:5 OK, 2 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 20 2025
R-4.5-winNOTEJan 20 2025
R-4.5-linuxNOTEJan 20 2025
R-4.4-winOKJan 20 2025
R-4.4-macOKJan 20 2025
R-4.3-winOKJan 20 2025
R-4.3-macOKJan 20 2025

Exports:.DollarNames.RangedSummarizedExperiment.DollarNames.SummarizedExperimentacbindarbindas.data.frameassayassay<-assayNamesassayNames<-assaysAssaysassays<-cbindcoercecolDatacolData<-colnamesComparecoveragedisjointBinsdistancedistanceToNearestduplicatedelementMetadataelementMetadata<-endend<-findOverlapsflankfollowgeneRangeMapperhorizontal_slot_namesis.unsortedisDisjointmakeSummarizedExperimentFromDataFramemakeSummarizedExperimentFromExpressionSetmakeSummarizedExperimentFromLoommatchmcolsmcols<-mergemetadata<-naiveRangeMappernarrowncolnearestnroworderparallel_slot_namespcompareprecedeprobeRangeMapperpromotersrangesranges<-rankrbindrealizeresizerestrictrowDatarowData<-rownamesrowRangesrowRanges<-saveRDSseqinfoseqinfo<-seqnamesseqnames<-shiftshowshowAsCellsortstartstart<-strandstrand<-subsetSummarizedExperimentterminatorstrimupdateObjectvaluesvalues<-vertical_slot_nameswidthwidth<-

Dependencies:abindaskpassBiobaseBiocGenericscrayoncurlDelayedArraygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6S4ArraysS4VectorsSparseArraysysUCSC.utilsXVector

SummarizedExperiment for Coordinating Experimental Assays, Samples, and Regions of Interest

Martin Morgan, Valerie Obenchain, Jim Hester, Hervé Pagès

Rendered fromSummarizedExperiment.Rmdusingknitr::rmarkdownon Jan 20 2025.

Last update: 2024-01-05
Started: 2015-05-14

Extending the SummarizedExperiment class

Aaron Lun

Rendered fromExtensions.Rmdusingknitr::rmarkdownon Jan 20 2025.

Last update: 2018-10-30
Started: 2018-05-03

Readme and manuals

Help Manual

Help pageTopics
Assays objectsacbind,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 objectcoverage coverage,RangedSummarizedExperiment-method coverage-methods
Finding overlapping ranges in RangedSummarizedExperiment objectsfindOverlaps findOverlaps,RangedSummarizedExperiment,RangedSummarizedExperiment-method findOverlaps,RangedSummarizedExperiment,Vector-method findOverlaps,Vector,RangedSummarizedExperiment-method findOverlaps-methods
Inter range transformations of a RangedSummarizedExperiment objectdisjointBins disjointBins,RangedSummarizedExperiment-method inter-range-methods isDisjoint isDisjoint,RangedSummarizedExperiment-method
Intra range transformations of a RangedSummarizedExperiment objectflank 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 DataFramemakeSummarizedExperimentFromDataFrame
Make a RangedSummarizedExperiment object from an ExpressionSet and vice-versacoerce,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 filemakeSummarizedExperimentFromLoom
Finding the nearest range neighbor in RangedSummarizedExperiment objectsdistance 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 objectsclass: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