A container (S4 class) for matrix-like assays

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Documentation for package ‘SummarizedExperiment’ version 1.38.1

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

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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