# A container (S4 class) for matrix-like assays

## Documentation for package ‘SummarizedExperiment’ version 1.40.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A C D E F G H I L M N O P R S T U V W misc

## -- A --

acbind-method | Assays objects
arbind-method | Assays objects
assay | SummarizedExperiment objects
assay-method | SummarizedExperiment objects
assay<- | SummarizedExperiment objects
assay<--method | SummarizedExperiment objects
assayNames | SummarizedExperiment objects
assayNames-method | SummarizedExperiment objects
assayNames<- | SummarizedExperiment objects
assayNames<--method | SummarizedExperiment objects
Assays | Assays objects
assays | SummarizedExperiment objects
Assays-class | Assays objects
assays-method | SummarizedExperiment objects
assays<- | SummarizedExperiment objects
assays<--method | SummarizedExperiment objects
AssaysInEnv | Assays objects
AssaysInEnv-class | Assays objects
Assays_OR_NULL | SummarizedExperiment objects
Assays_OR_NULL-class | SummarizedExperiment objects

## -- C --

cbind-method | Assays objects
cbind-method | SummarizedExperiment objects
class:Assays | Assays objects
class:AssaysInEnv | Assays objects
class:Assays_OR_NULL | SummarizedExperiment objects
class:RangedSummarizedExperiment | RangedSummarizedExperiment objects
class:ShallowData | Assays objects
class:ShallowSimpleListAssays | Assays objects
class:SimpleAssays | Assays objects
class:SummarizedExperiment | SummarizedExperiment objects
coerce-method | Assays objects
coerce-method | RangedSummarizedExperiment objects
coerce-method | Make a RangedSummarizedExperiment object from an ExpressionSet and vice-versa
colData | SummarizedExperiment objects
colData-method | SummarizedExperiment objects
colData<- | SummarizedExperiment objects
colData<--method | SummarizedExperiment objects
colnames-method | SummarizedExperiment objects
combineCols | SummarizedExperiment objects
combineCols-method | SummarizedExperiment objects
combineRows | SummarizedExperiment objects
combineRows-method | SummarizedExperiment objects
Compare-method | RangedSummarizedExperiment objects
coverage | Coverage of a RangedSummarizedExperiment object
coverage-method | Coverage of a RangedSummarizedExperiment object
coverage-methods | Coverage of a RangedSummarizedExperiment object

## -- D --

dim-method | Assays objects
dimnames<--method | RangedSummarizedExperiment objects
dimnames<--method | SummarizedExperiment objects
disjointBins | Inter range transformations of a RangedSummarizedExperiment object
disjointBins-method | Inter range transformations of a RangedSummarizedExperiment object
distance | Finding the nearest range neighbor in RangedSummarizedExperiment objects
distance-method | Finding the nearest range neighbor in RangedSummarizedExperiment objects
distanceToNearest | Finding the nearest range neighbor in RangedSummarizedExperiment objects
distanceToNearest-method | Finding the nearest range neighbor in RangedSummarizedExperiment objects
duplicated-method | RangedSummarizedExperiment objects

## -- E --

elementMetadata-method | RangedSummarizedExperiment objects
elementMetadata<--method | RangedSummarizedExperiment objects
end-method | RangedSummarizedExperiment objects
end<--method | RangedSummarizedExperiment objects

## -- F --

findOverlaps | Finding overlapping ranges in RangedSummarizedExperiment objects
findOverlaps-method | Finding overlapping ranges in RangedSummarizedExperiment objects
findOverlaps-methods | Finding overlapping ranges in RangedSummarizedExperiment objects
flank | Intra range transformations of a RangedSummarizedExperiment object
flank-method | Intra range transformations of a RangedSummarizedExperiment object
follow | Finding the nearest range neighbor in RangedSummarizedExperiment objects
follow-method | Finding the nearest range neighbor in RangedSummarizedExperiment objects

## -- G --

geneRangeMapper | Make a RangedSummarizedExperiment object from an ExpressionSet and vice-versa
getListElement-method | Assays objects
granges-method | RangedSummarizedExperiment objects

## -- H --

horizontal_slot_names-method | SummarizedExperiment objects

## -- I --

inter-range-methods | Inter range transformations of a RangedSummarizedExperiment object
intra-range-methods | Intra range transformations of a RangedSummarizedExperiment object
is.unsorted-method | RangedSummarizedExperiment objects
isDisjoint | Inter range transformations of a RangedSummarizedExperiment object
isDisjoint-method | Inter range transformations of a RangedSummarizedExperiment object

## -- L --

length-method | Assays objects
length-method | SummarizedExperiment objects

## -- M --

makeSummarizedExperimentFromDataFrame | Make a RangedSummarizedExperiment from a data.frame or DataFrame
makeSummarizedExperimentFromExpressionSet | Make a RangedSummarizedExperiment object from an ExpressionSet and vice-versa
makeSummarizedExperimentFromLoom | Make a SummarizedExperiment from a '.loom' hdf5 file
mcols-method | RangedSummarizedExperiment objects
mcols<--method | RangedSummarizedExperiment objects

## -- N --

naiveRangeMapper | Make a RangedSummarizedExperiment object from an ExpressionSet and vice-versa
names-method | Assays objects
names-method | RangedSummarizedExperiment objects
names-method | SummarizedExperiment objects
names<--method | Assays objects
names<--method | RangedSummarizedExperiment objects
names<--method | SummarizedExperiment objects
narrow | Intra range transformations of a RangedSummarizedExperiment object
narrow-method | Intra range transformations of a RangedSummarizedExperiment object
ncol-method | SummarizedExperiment objects
nearest | Finding the nearest range neighbor in RangedSummarizedExperiment objects
nearest-method | Finding the nearest range neighbor in RangedSummarizedExperiment objects
nearest-methods | Finding the nearest range neighbor in RangedSummarizedExperiment objects
nrow-method | SummarizedExperiment objects

## -- O --

order-method | RangedSummarizedExperiment objects

## -- P --

parallel_slot_names-method | RangedSummarizedExperiment objects
parallel_slot_names-method | SummarizedExperiment objects
pcompare-method | RangedSummarizedExperiment objects
precede | Finding the nearest range neighbor in RangedSummarizedExperiment objects
precede-method | Finding the nearest range neighbor in RangedSummarizedExperiment objects
probeRangeMapper | Make a RangedSummarizedExperiment object from an ExpressionSet and vice-versa
promoters | Intra range transformations of a RangedSummarizedExperiment object
promoters-method | Intra range transformations of a RangedSummarizedExperiment object

## -- R --

RangedSummarizedExperiment | RangedSummarizedExperiment objects
RangedSummarizedExperiment-class | RangedSummarizedExperiment objects
ranges-method | RangedSummarizedExperiment objects
ranges<--method | RangedSummarizedExperiment objects
rank-method | RangedSummarizedExperiment objects
rbind-method | Assays objects
rbind-method | SummarizedExperiment objects
realize-method | SummarizedExperiment objects
resize | Intra range transformations of a RangedSummarizedExperiment object
resize-method | Intra range transformations of a RangedSummarizedExperiment object
restrict | Intra range transformations of a RangedSummarizedExperiment object
restrict-method | Intra range transformations of a RangedSummarizedExperiment object
rowData | SummarizedExperiment objects
rowData-method | SummarizedExperiment objects
rowData<- | SummarizedExperiment objects
rowData<--method | SummarizedExperiment objects
rownames-method | SummarizedExperiment objects
rowRanges | RangedSummarizedExperiment objects
rowRanges-method | RangedSummarizedExperiment objects
rowRanges<- | RangedSummarizedExperiment objects
rowRanges<--method | RangedSummarizedExperiment objects

## -- S --

saveRDS-method | SummarizedExperiment objects
seqinfo-method | RangedSummarizedExperiment objects
seqinfo<--method | RangedSummarizedExperiment objects
seqnames-method | RangedSummarizedExperiment objects
setListElement-method | Assays objects
ShallowData | Assays objects
ShallowData-class | Assays objects
ShallowSimpleListAssays | Assays objects
ShallowSimpleListAssays-class | Assays objects
shift | Intra range transformations of a RangedSummarizedExperiment object
shift-method | Intra range transformations of a RangedSummarizedExperiment object
show-method | SummarizedExperiment objects
showAsCell-method | SummarizedExperiment objects
SimpleAssays | Assays objects
SimpleAssays-class | Assays objects
sort-method | RangedSummarizedExperiment objects
split-method | RangedSummarizedExperiment objects
start-method | RangedSummarizedExperiment objects
start<--method | RangedSummarizedExperiment objects
strand-method | RangedSummarizedExperiment objects
strand<--method | RangedSummarizedExperiment objects
subset-method | RangedSummarizedExperiment objects
subset-method | SummarizedExperiment objects
SummarizedExperiment | SummarizedExperiment objects
SummarizedExperiment-class | SummarizedExperiment objects

## -- T --

terminators | Intra range transformations of a RangedSummarizedExperiment object
terminators-method | Intra range transformations of a RangedSummarizedExperiment object
trim-method | Intra range transformations of a RangedSummarizedExperiment object

## -- U --

updateObject-method | Assays objects
updateObject-method | RangedSummarizedExperiment objects
updateObject-method | SummarizedExperiment objects

## -- V --

vertical_slot_names-method | SummarizedExperiment objects

## -- W --

width-method | RangedSummarizedExperiment objects
width<--method | RangedSummarizedExperiment objects

## -- misc --

$-method | SummarizedExperiment objects
$<--method | SummarizedExperiment objects
[-method | Assays objects
[-method | SummarizedExperiment objects
[<--method | Assays objects
[<--method | SummarizedExperiment objects
[[-method | SummarizedExperiment objects
[[<--method | SummarizedExperiment objects