Package: SummarizedExperiment 1.35.1

Hervé Pagès

SummarizedExperiment: SummarizedExperiment container

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]

# 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-1.35.0(bioc 3.20)SummarizedExperiment-1.34.0(bioc 3.19)

bioconductor-package

87 exports 12.48 score 27 dependencies 1129 dependents 52 mentions

Last updated 13 days agofrom:c5b7ca2f8d

Exports:.DollarNames.RangedSummarizedExperiment .DollarNames.SummarizedExperiment acbind arbind as.data.frame assay assay<-assayNames assayNames<-assays Assays assays<-cbind coerce colData colData<-colnames Compare coverage disjointBins distance distanceToNearest duplicated elementMetadata elementMetadata<-end end<-findOverlaps flank follow geneRangeMapper horizontal_slot_names is.unsorted isDisjoint makeSummarizedExperimentFromDataFrame makeSummarizedExperimentFromExpressionSet makeSummarizedExperimentFromLoom match mcols mcols<-merge metadata<-naiveRangeMapper narrow ncol nearest nrow order parallel_slot_names pcompare precede probeRangeMapper promoters ranges ranges<-rank rbind realize resize restrict rowData rowData<-rownames rowRanges rowRanges<-seqinfo seqinfo<-seqnames seqnames<-shift show showAsCell sort start start<-strand strand<-subset SummarizedExperiment terminators trim updateObject values values<-vertical_slot_names width width<-

Dependencies:abind askpass Biobase BiocGenerics crayon curl DelayedArray GenomeInfoDb GenomeInfoDbData GenomicRanges httr IRanges jsonlite lattice Matrix MatrixGenerics matrixStats mime openssl R6 S4Arrays S4Vectors SparseArray sys UCSC.utils XVector zlibbioc

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

Martin Morgan, Valerie Obenchain, Jim Hester, Hervé Pagès

Rendered fromSummarizedExperiment.Rmdusingknitr::rmarkdownon Jun 29 2024.

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

Extending the SummarizedExperiment class

Aaron Lun

Rendered fromExtensions.Rmdusingknitr::rmarkdownon Jun 29 2024.

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

Citation

Development and contributors

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 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