SummarizedExperiment: SummarizedExperiment container
Version 1.6.1

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
Bioconductor views Annotation Coverage Genetics GenomeAnnotation Infrastructure Sequencing
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version1.6.1
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SummarizedExperiment")

Getting started

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

Popular man pages

coverage-methods: Coverage of a RangedSummarizedExperiment object
findOverlaps-methods: Finding overlapping ranges in RangedSummarizedExperiment...
makeSummarizedExperimentFromDataFrame: Make a RangedSummarizedExperiment from a data.frame or...
nearest-methods: Finding the nearest range neighbor in...
RangedSummarizedExperiment-class: RangedSummarizedExperiment objects
saveHDF5SummarizedExperiment: Save/load a HDF5-based SummarizedExperiment object
SummarizedExperiment-class: SummarizedExperiment objects
See all...

All man pages Function index File listing

Man pages

Assays-class: Assays objects
coverage-methods: Coverage of a RangedSummarizedExperiment object
findOverlaps-methods: Finding overlapping ranges in RangedSummarizedExperiment...
inter-range-methods: Inter range transformations of a RangedSummarizedExperiment...
intra-range-methods: Intra range transformations of a RangedSummarizedExperiment...
makeSummarizedExperimentFromDataFrame: Make a RangedSummarizedExperiment from a data.frame or...
makeSummarizedExperimentFromExpressionSet: Make a RangedSummarizedExperiment object from an...
nearest-methods: Finding the nearest range neighbor in...
RangedSummarizedExperiment-class: RangedSummarizedExperiment objects
readKallisto: Input kallisto or kallisto bootstrap results.
saveHDF5SummarizedExperiment: Save/load a HDF5-based SummarizedExperiment object
SummarizedExperiment-class: SummarizedExperiment objects

Functions

$,SummarizedExperiment-method Man page
$<-,SummarizedExperiment-method Man page
Assays Man page Source code
Assays-class Man page
AssaysInEnv Man page
AssaysInEnv-class Man page
Compare,ANY,RangedSummarizedExperiment-method Man page
Compare,RangedSummarizedExperiment,ANY-method Man page
Compare,RangedSummarizedExperiment,RangedSummarizedExperiment-me Man page
DollarNames.SummarizedExperiment Source code
KALLISTO_ASSAYS Man page
RangedSummarizedExperiment Man page
RangedSummarizedExperiment-class Man page
RangedSummarizedExperiment.Compare Source code
RangedSummarizedExperiment.pcompare Source code
ShallowData Man page
ShallowData-class Man page
ShallowSimpleListAssays Man page
ShallowSimpleListAssays-class Man page
SimpleListAssays Man page
SimpleListAssays-class Man page
SummarizedExperiment Man page
SummarizedExperiment,ANY-method Man page
SummarizedExperiment,SimpleList-method Man page
SummarizedExperiment,list-method Man page
SummarizedExperiment,missing-method Man page
SummarizedExperiment-class Man page
SummarizedExperiment.assays.replace Source code
SummarizedExperiment.charbound Source code
SummarizedExperiment.rowRanges.replace Source code
[,Assays,ANY,ANY,ANY-method Man page
[,Assays,ANY-method Man page
[,SummarizedExperiment,ANY,ANY,ANY-method Man page
[,SummarizedExperiment,ANY-method Man page
[,SummarizedExperiment-method Man page
[<-,Assays,ANY,ANY,ANY-method Man page
[<-,SummarizedExperiment,ANY,ANY,SummarizedExperiment-method Man page
[[,Assays,ANY,ANY-method Man page
[[,AssaysInEnv,ANY,ANY-method Man page
[[,SummarizedExperiment,ANY,missing-method Man page
[[<-,Assays,ANY,ANY-method Man page
[[<-,AssaysInEnv,ANY,ANY-method Man page
[[<-,SummarizedExperiment,ANY,missing-method Man page
acbind,Matrix-method Man page
arbind,Matrix-method Man page
assay Man page
assay,SummarizedExperiment,character-method Man page
assay,SummarizedExperiment,missing-method Man page
assay,SummarizedExperiment,numeric-method Man page
assay<- Man page
assay<-,SummarizedExperiment,character-method Man page
assay<-,SummarizedExperiment,missing-method Man page
assay<-,SummarizedExperiment,numeric-method Man page
assayNames Man page
assayNames,SummarizedExperiment-method Man page
assayNames<- Man page
assayNames<-,SummarizedExperiment,character-method Man page
assays Man page
assays,SummarizedExperiment-method Man page
assays<- Man page
assays<-,SummarizedExperiment,SimpleList-method Man page
assays<-,SummarizedExperiment,list-method Man page
bind_Assays Source code
cbind,Assays-method Man page
cbind,SummarizedExperiment-method Man page
cbind.DataFrame Source code
cbind.SummarizedExperiment Source code
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
close Source code
close.H5IdComponent Source code
close.connection Source code
close.list Source code
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 Source code
colData,SummarizedExperiment-method Man page
colData<- Man page
colData<-,SummarizedExperiment,DataFrame-method Man page
compare Source code
coverage Man page
coverage,RangedSummarizedExperiment-method Man page
coverage-methods Man page
create_dir Source code
dim,Assays-method Man page
dim,SummarizedExperiment-method Man page
dimnames,RangedSummarizedExperiment-method Man page
dimnames,SummarizedExperiment-method Man page
dimnames<-,RangedSummarizedExperiment,list-method Man page
dimnames<-,SummarizedExperiment,NULL-method Man page
dimnames<-,SummarizedExperiment,list-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
extract_Assays_subset Source code
findOverlaps Man page
findOverlaps,RangedSummarizedExperiment,RangedSummarizedExperime Man page
findOverlaps,RangedSummarizedExperiment,Vector-method Man page
findOverlaps,Vector,RangedSummarizedExperiment-method Man page
findOverlaps-methods 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
from_AnnotatedDataFrame_to_DataFrame Source code
from_DataFrame_to_AnnotatedDataFrame Source code
from_GRangesList_to_FeatureData Source code
from_GRanges_to_FeatureData Source code
from_RangedSummarizedExperiment_to_SummarizedExperiment Source code
from_SummarizedExperiment_to_RangedSummarizedExperiment Source code
from_old_SummarizedExperiment_to_RangedSummarizedExperiment Source code
from_rowRanges_to_FeatureData Source code
geneRangeMapper Man page Source code
get_colnames_from_assays Source code
get_rownames_from_assays Source code
granges,RangedSummarizedExperiment-method Man page
has_old_SummarizedExperiment_internal_structure Source code
inter-range-methods Man page
intra-range-methods Man page
is.unsorted,RangedSummarizedExperiment-method Man page
isDisjoint Man page
isDisjoint,RangedSummarizedExperiment-method Man page
length,Assays-method Man page
length,AssaysInEnv-method Man page
length,SummarizedExperiment-method Man page
loadHDF5SummarizedExperiment Man page Source code
makeSummarizedExperimentFromDataFrame Man page Source code
makeSummarizedExperimentFromExpressionSet Man page Source code
mcols,RangedSummarizedExperiment-method Man page
mcols<-,RangedSummarizedExperiment-method Man page
naiveRangeMapper Man page Source code
names,Assays-method Man page
names,AssaysInEnv-method Man page
names,RangedSummarizedExperiment-method Man page
names,SummarizedExperiment-method Man page
names<-,Assays-method Man page
names<-,AssaysInEnv-method Man page
names<-,RangedSummarizedExperiment-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,RangedSummarizedExperiment,ANY-method Man page
nearest,RangedSummarizedExperiment,RangedSummarizedExperiment-me Man page
nearest-methods Man page
new_RangedSummarizedExperiment Source code
new_SummarizedExperiment Source code
normarg_assays Source code
open Source code
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 Source code
promoters Man page
promoters,RangedSummarizedExperiment-method 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
rbind.SummarizedExperiment Source code
read Source code
read.H5IdComponent Source code
read.connection Source code
readIds Source code
readKallisto Man page Source code
readKallistoBootstrap Man page Source code
realize,SummarizedExperiment-method Man page
replaceROWS,SummarizedExperiment-method Man page
replace_Assays_subset Source code
resize Man page
resize,RangedSummarizedExperiment-method Man page
restrict Man page
restrict,RangedSummarizedExperiment-method Man page
rowData Man page
rowData,SummarizedExperiment-method Man page
rowData<- Man page
rowData<-,SummarizedExperiment-method Man page
rowRanges Man page
rowRanges,RangedSummarizedExperiment-method Man page
rowRanges<- Man page
rowRanges<-,SummarizedExperiment,GRangesList-method Man page
rowRanges<-,SummarizedExperiment,GenomicRanges-method Man page
saveHDF5SummarizedExperiment Man page Source code
seqinfo,RangedSummarizedExperiment-method Man page
seqinfo<-,RangedSummarizedExperiment-method Man page
seqnames,RangedSummarizedExperiment-method Man page
shift Man page
shift,RangedSummarizedExperiment-method Man page
shorten_h5_paths Source code
show,SummarizedExperiment-method 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
stop_if_bad_dir Source code
strand,RangedSummarizedExperiment-method Man page
strand<-,RangedSummarizedExperiment,ANY-method Man page
subset,RangedSummarizedExperiment-method Man page
test Source code
trim,RangedSummarizedExperiment-method Man page
updateObject,SummarizedExperiment-method Man page
update_old_SummarizedExperiment Source code
valid.Assays Source code
valid.RangedSummarizedExperiment Source code
valid.SummarizedExperiment Source code
valid.SummarizedExperiment.assays_dim Source code
valid.SummarizedExperiment.assays_ncol Source code
valid.SummarizedExperiment.assays_nrow Source code
width,RangedSummarizedExperiment-method Man page
width<-,RangedSummarizedExperiment-method Man page
write_h5_assays Source code

Files

DESCRIPTION
NAMESPACE
NEWS
NOTES
R
R/Assays-class.R
R/RangedSummarizedExperiment-class.R
R/SummarizedExperiment-class.R
R/coverage-methods.R
R/findOverlaps-methods.R
R/inter-range-methods.R
R/intra-range-methods.R
R/makeSummarizedExperimentFromDataFrame.R
R/makeSummarizedExperimentFromExpressionSet.R
R/nearest-methods.R
R/readKallisto.R
R/saveHDF5SummarizedExperiment.R
R/zzz.R
build
build/vignette.rds
inst
inst/doc
inst/doc/SummarizedExperiment.R
inst/doc/SummarizedExperiment.Rmd
inst/doc/SummarizedExperiment.html
inst/extdata
inst/extdata/kallisto
inst/extdata/kallisto/abundance.h5
inst/extdata/kallisto/abundance.tsv
inst/extdata/kallisto/abundance.txt
inst/extdata/kallisto/run_info.json
inst/scripts
inst/scripts/Find_and_update_objects
inst/scripts/Find_and_update_objects/README
inst/scripts/Find_and_update_objects/collect_rda_objects_to_update.R
inst/scripts/Find_and_update_objects/data_store_RDA_OBJECTS_TO_UPDATE
inst/scripts/Find_and_update_objects/pkgs_RDA_OBJECTS_TO_UPDATE
inst/scripts/Find_and_update_objects/scan_rda_files.R
inst/scripts/Find_and_update_objects/update_rda_objects.R
inst/unitTests
inst/unitTests/test_Assays-class.R
inst/unitTests/test_RangedSummarizedExperiment-class.R
inst/unitTests/test_SummarizedExperiment-class.R
inst/unitTests/test_coverage-methods.R
inst/unitTests/test_findOverlaps-methods.R
inst/unitTests/test_inter-range-methods.R
inst/unitTests/test_intra-range-methods.R
inst/unitTests/test_makeSummarizedExperimentFromDataFrame.R
inst/unitTests/test_makeSummarizedExperimentFromExpressionSet.R
inst/unitTests/test_nearest-methods.R
man
man/Assays-class.Rd
man/RangedSummarizedExperiment-class.Rd
man/SummarizedExperiment-class.Rd
man/coverage-methods.Rd
man/findOverlaps-methods.Rd
man/inter-range-methods.Rd
man/intra-range-methods.Rd
man/makeSummarizedExperimentFromDataFrame.Rd
man/makeSummarizedExperimentFromExpressionSet.Rd
man/nearest-methods.Rd
man/readKallisto.Rd
man/saveHDF5SummarizedExperiment.Rd
tests
tests/run_unitTests.R
vignettes
vignettes/SummarizedExperiment.Rmd
SummarizedExperiment documentation built on May 20, 2017, 11 p.m.

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