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.

AuthorMartin Morgan, Valerie Obenchain, Jim Hester, Hervé Pagès
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version1.4.0

View on Bioconductor

Functions

acbind,Matrix-method Man page
arbind,Matrix-method Man page
assay Man page
assay<- Man page
assayNames Man page
assayNames<- Man page
assayNames<-,SummarizedExperiment,character-method Man page
assayNames,SummarizedExperiment-method Man page
assays Man page
assays<- Man page
Assays Man page
[<-,Assays,ANY,ANY,ANY-method Man page
[,Assays,ANY,ANY,ANY-method Man page
[[<-,Assays,ANY,ANY-method Man page
[[,Assays,ANY,ANY-method Man page
[,Assays,ANY-method Man page
Assays-class Man page
AssaysInEnv Man page
[[<-,AssaysInEnv,ANY,ANY-method Man page
[[,AssaysInEnv,ANY,ANY-method Man page
AssaysInEnv-class Man page
assays<-,SummarizedExperiment,list-method Man page
assays,SummarizedExperiment-method Man page
assays<-,SummarizedExperiment,SimpleList-method Man page
assay<-,SummarizedExperiment,character-method Man page
assay,SummarizedExperiment,character-method Man page
assay<-,SummarizedExperiment,missing-method Man page
assay,SummarizedExperiment,missing-method Man page
assay<-,SummarizedExperiment,numeric-method Man page
assay,SummarizedExperiment,numeric-method Man page
cbind,Assays-method Man page
cbind,SummarizedExperiment-method Man page
class:Assays Man page
class:AssaysInEnv Man page
class:RangedSummarizedExperiment Man page
class:ShallowData Man page
class:ShallowSimpleListAssays Man page
class:SimpleListAssays Man page
class:SummarizedExperiment Man page
class:SummarizedExperiment0 Man page
coerce,AssaysInEnv,SimpleList-method Man page
coerce,ExpressionSet,RangedSummarizedExperiment-method Man page
coerce,RangedSummarizedExperiment,ExpressionSet-method Man page
coerce,RangedSummarizedExperiment,SummarizedExperiment-method Man page
coerce,ShallowSimpleListAssays,SimpleList-method Man page
coerce,SimpleList,AssaysInEnv-method Man page
coerce,SimpleList,ShallowSimpleListAssays-method Man page
coerce,SummarizedExperiment,ExpressionSet-method Man page
coerce,SummarizedExperiment,RangedSummarizedExperiment-method Man page
colData Man page
colData<- Man page
colData<-,SummarizedExperiment,DataFrame-method Man page
colData,SummarizedExperiment-method Man page
Compare,ANY,RangedSummarizedExperiment-method Man page
Compare,RangedSummarizedExperiment,ANY-method Man page
Compare,RangedSummarizedExperiment,RangedSummarizedExperiment-me Man page
coverage Man page
coverage-methods Man page
coverage,RangedSummarizedExperiment-method Man page
dim,Assays-method Man page
dimnames<-,RangedSummarizedExperiment,list-method Man page
dimnames,RangedSummarizedExperiment-method Man page
dimnames<-,SummarizedExperiment,list-method Man page
dimnames,SummarizedExperiment-method Man page
dimnames<-,SummarizedExperiment,NULL-method Man page
dim,SummarizedExperiment-method Man page
disjointBins Man page
disjointBins,RangedSummarizedExperiment-method Man page
distance Man page
distance,ANY,RangedSummarizedExperiment-method Man page
distance,RangedSummarizedExperiment,ANY-method Man page
distance,RangedSummarizedExperiment,RangedSummarizedExperiment-m Man page
distanceToNearest Man page
distanceToNearest,ANY,RangedSummarizedExperiment-method Man page
distanceToNearest,RangedSummarizedExperiment,ANY-method Man page
distanceToNearest,RangedSummarizedExperiment,RangedSummarizedExp Man page
duplicated,RangedSummarizedExperiment-method Man page
elementMetadata<-,RangedSummarizedExperiment-method Man page
elementMetadata,RangedSummarizedExperiment-method Man page
end<-,RangedSummarizedExperiment-method Man page
end,RangedSummarizedExperiment-method Man page
extractROWS,SummarizedExperiment,ANY-method Man page
findOverlaps Man page
findOverlaps-methods Man page
findOverlaps,RangedSummarizedExperiment,RangedSummarizedExperime Man page
findOverlaps,RangedSummarizedExperiment,Vector-method Man page
findOverlaps,Vector,RangedSummarizedExperiment-method Man page
flank Man page
flank,RangedSummarizedExperiment-method Man page
follow Man page
follow,ANY,RangedSummarizedExperiment-method Man page
follow,RangedSummarizedExperiment,ANY-method Man page
follow,RangedSummarizedExperiment,RangedSummarizedExperiment-met Man page
geneRangeMapper Man page
granges,RangedSummarizedExperiment-method Man page
inter-range-methods Man page
intra-range-methods Man page
isDisjoint Man page
isDisjoint,RangedSummarizedExperiment-method Man page
is.unsorted,RangedSummarizedExperiment-method Man page
KALLISTO_ASSAYS Man page
length,AssaysInEnv-method Man page
length,Assays-method Man page
length,SummarizedExperiment-method Man page
makeSummarizedExperimentFromDataFrame Man page
makeSummarizedExperimentFromExpressionSet Man page
mcols<-,RangedSummarizedExperiment-method Man page
mcols,RangedSummarizedExperiment-method Man page
naiveRangeMapper Man page
names<-,AssaysInEnv-method Man page
names,AssaysInEnv-method Man page
names<-,Assays-method Man page
names,Assays-method Man page
names<-,RangedSummarizedExperiment-method Man page
names,RangedSummarizedExperiment-method Man page
names<-,SummarizedExperiment-method Man page
names,SummarizedExperiment-method Man page
narrow Man page
narrow,RangedSummarizedExperiment-method Man page
nearest Man page
nearest,ANY,RangedSummarizedExperiment-method Man page
nearest-methods Man page
nearest,RangedSummarizedExperiment,ANY-method Man page
nearest,RangedSummarizedExperiment,RangedSummarizedExperiment-me Man page
order,RangedSummarizedExperiment-method Man page
pcompare,ANY,RangedSummarizedExperiment-method Man page
pcompare,RangedSummarizedExperiment,ANY-method Man page
pcompare,RangedSummarizedExperiment,RangedSummarizedExperiment-m Man page
precede Man page
precede,ANY,RangedSummarizedExperiment-method Man page
precede,RangedSummarizedExperiment,ANY-method Man page
precede,RangedSummarizedExperiment,RangedSummarizedExperiment-me Man page
probeRangeMapper Man page
promoters Man page
promoters,RangedSummarizedExperiment-method Man page
RangedSummarizedExperiment Man page
RangedSummarizedExperiment-class Man page
ranges<-,RangedSummarizedExperiment-method Man page
ranges,RangedSummarizedExperiment-method Man page
rank,RangedSummarizedExperiment-method Man page
rbind,Assays-method Man page
rbind,SummarizedExperiment-method Man page
readKallisto Man page
readKallistoBootstrap Man page
replaceROWS,SummarizedExperiment-method Man page
resize Man page
resize,RangedSummarizedExperiment-method Man page
restrict Man page
restrict,RangedSummarizedExperiment-method Man page
rowData Man page
rowData<- Man page
rowData<-,SummarizedExperiment-method Man page
rowData,SummarizedExperiment-method Man page
rowRanges Man page
rowRanges<- Man page
rowRanges,RangedSummarizedExperiment-method Man page
rowRanges<-,SummarizedExperiment,GenomicRanges-method Man page
rowRanges<-,SummarizedExperiment,GRangesList-method Man page
seqinfo<-,RangedSummarizedExperiment-method Man page
seqinfo,RangedSummarizedExperiment-method Man page
seqnames,RangedSummarizedExperiment-method Man page
ShallowData Man page
ShallowData-class Man page
ShallowSimpleListAssays Man page
ShallowSimpleListAssays-class Man page
shift Man page
shift,RangedSummarizedExperiment-method Man page
show,SummarizedExperiment-method Man page
SimpleListAssays Man page
SimpleListAssays-class Man page
sort,RangedSummarizedExperiment-method Man page
split,RangedSummarizedExperiment,ANY-method Man page
split,RangedSummarizedExperiment-method Man page
start<-,RangedSummarizedExperiment-method Man page
start,RangedSummarizedExperiment-method Man page
strand<-,RangedSummarizedExperiment,ANY-method Man page
strand,RangedSummarizedExperiment-method Man page
subset,RangedSummarizedExperiment-method Man page
SummarizedExperiment Man page
SummarizedExperiment0 Man page
SummarizedExperiment0-class Man page
[,SummarizedExperiment,ANY,ANY,ANY-method Man page
[<-,SummarizedExperiment,ANY,ANY,SummarizedExperiment-method Man page
[,SummarizedExperiment,ANY-method Man page
SummarizedExperiment,ANY-method Man page
[[<-,SummarizedExperiment,ANY,missing-method Man page
[[,SummarizedExperiment,ANY,missing-method Man page
SummarizedExperiment-class Man page
SummarizedExperiment,list-method Man page
[,SummarizedExperiment-method Man page
$<-,SummarizedExperiment-method Man page
$,SummarizedExperiment-method Man page
SummarizedExperiment,missing-method Man page
SummarizedExperiment,SimpleList-method Man page
trim,RangedSummarizedExperiment-method Man page
updateObject,SummarizedExperiment-method Man page
width<-,RangedSummarizedExperiment-method Man page
width,RangedSummarizedExperiment-method Man page

Files

SummarizedExperiment/DESCRIPTION
SummarizedExperiment/NAMESPACE
SummarizedExperiment/NEWS
SummarizedExperiment/R
SummarizedExperiment/R/Assays-class.R SummarizedExperiment/R/RangedSummarizedExperiment-class.R SummarizedExperiment/R/SummarizedExperiment-class.R SummarizedExperiment/R/coverage-methods.R SummarizedExperiment/R/findOverlaps-methods.R SummarizedExperiment/R/inter-range-methods.R SummarizedExperiment/R/intra-range-methods.R SummarizedExperiment/R/makeSummarizedExperimentFromDataFrame.R SummarizedExperiment/R/makeSummarizedExperimentFromExpressionSet.R SummarizedExperiment/R/nearest-methods.R SummarizedExperiment/R/readKallisto.R SummarizedExperiment/R/zzz.R
SummarizedExperiment/TODO
SummarizedExperiment/build
SummarizedExperiment/build/vignette.rds
SummarizedExperiment/inst
SummarizedExperiment/inst/doc
SummarizedExperiment/inst/doc/SummarizedExperiment.R
SummarizedExperiment/inst/doc/SummarizedExperiment.Rmd
SummarizedExperiment/inst/doc/SummarizedExperiment.html
SummarizedExperiment/inst/extdata
SummarizedExperiment/inst/extdata/kallisto
SummarizedExperiment/inst/extdata/kallisto/abundance.h5
SummarizedExperiment/inst/extdata/kallisto/abundance.tsv
SummarizedExperiment/inst/extdata/kallisto/abundance.txt
SummarizedExperiment/inst/extdata/kallisto/run_info.json
SummarizedExperiment/inst/scripts
SummarizedExperiment/inst/scripts/Find_and_update_objects
SummarizedExperiment/inst/scripts/Find_and_update_objects/README
SummarizedExperiment/inst/scripts/Find_and_update_objects/collect_rda_objects_to_update.R
SummarizedExperiment/inst/scripts/Find_and_update_objects/data_store_RDA_OBJECTS_TO_UPDATE
SummarizedExperiment/inst/scripts/Find_and_update_objects/pkgs_RDA_OBJECTS_TO_UPDATE
SummarizedExperiment/inst/scripts/Find_and_update_objects/scan_rda_files.R
SummarizedExperiment/inst/scripts/Find_and_update_objects/update_rda_objects.R
SummarizedExperiment/inst/unitTests
SummarizedExperiment/inst/unitTests/test_Assays-class.R
SummarizedExperiment/inst/unitTests/test_RangedSummarizedExperiment-class.R
SummarizedExperiment/inst/unitTests/test_SummarizedExperiment-class.R
SummarizedExperiment/inst/unitTests/test_coverage-methods.R
SummarizedExperiment/inst/unitTests/test_findOverlaps-methods.R
SummarizedExperiment/inst/unitTests/test_inter-range-methods.R
SummarizedExperiment/inst/unitTests/test_intra-range-methods.R
SummarizedExperiment/inst/unitTests/test_makeSummarizedExperimentFromDataFrame.R
SummarizedExperiment/inst/unitTests/test_makeSummarizedExperimentFromExpressionSet.R
SummarizedExperiment/inst/unitTests/test_nearest-methods.R
SummarizedExperiment/man
SummarizedExperiment/man/Assays-class.Rd SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd SummarizedExperiment/man/SummarizedExperiment-class.Rd SummarizedExperiment/man/coverage-methods.Rd SummarizedExperiment/man/findOverlaps-methods.Rd SummarizedExperiment/man/inter-range-methods.Rd SummarizedExperiment/man/intra-range-methods.Rd SummarizedExperiment/man/makeSummarizedExperimentFromDataFrame.Rd SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd SummarizedExperiment/man/nearest-methods.Rd SummarizedExperiment/man/readKallisto.Rd
SummarizedExperiment/tests
SummarizedExperiment/tests/run_unitTests.R
SummarizedExperiment/vignettes
SummarizedExperiment/vignettes/SummarizedExperiment.Rmd

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