# S4 Classes for Single Cell Data

## Documentation for package ‘SingleCellExperiment’ version 1.16.0

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

## Help Pages

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

## -- A --

altExp | Alternative Experiment methods
altExp-method | Alternative Experiment methods
altExp<- | Alternative Experiment methods
altExp<--method | Alternative Experiment methods
altExpNames | Alternative Experiment methods
altExpNames-method | Alternative Experiment methods
altExpNames<- | Alternative Experiment methods
altExpNames<--method | Alternative Experiment methods
altExps | Alternative Experiment methods
altExps-method | Alternative Experiment methods
altExps<- | Alternative Experiment methods
altExps<--method | Alternative Experiment methods
applySCE | Applying over parts of a SingleCellExperiment
as.matrix-method | LinearEmbeddingMatrix getters/setters

## -- C --

c-method | Alternative Experiment methods
c-method | Row pair methods
cbind-method | LEM combining methods
cbind-method | Combining or subsetting SingleCellExperiment objects
cbind.reduced.dim.matrix | The reduced.dim.matrix class
check | Alternative Experiment methods
clearSizeFactors | Defunct methods
clearSpikes | Defunct methods
coerce-method | The SingleCellExperiment class
colData-method | Internal SingleCellExperiment functions
colLabels | Get or set column labels
colLabels-method | Get or set column labels
colLabels<- | Get or set column labels
colLabels<--method | Get or set column labels
colPair | Column pair methods
colPair-method | Column pair methods
colPair<- | Column pair methods
colPair<--method | Column pair methods
colPairNames | Column pair methods
colPairNames-method | Column pair methods
colPairNames<- | Column pair methods
colPairNames<--method | Column pair methods
colPairs | Column pair methods
colPairs-method | Column pair methods
colPairs<- | Column pair methods
colPairs<--method | Column pair methods
combineCols-method | Combining or subsetting SingleCellExperiment objects
complain. | Alternative Experiment methods
counts | Named assay getters and setters
counts-method | Named assay getters and setters
counts<- | Named assay getters and setters
counts<--method | Named assay getters and setters
cpm | Named assay getters and setters
cpm-method | Named assay getters and setters
cpm<- | Named assay getters and setters
cpm<--method | Named assay getters and setters

## -- D --

defunct | Defunct methods
dim-method | LinearEmbeddingMatrix getters/setters
dimnames-method | LinearEmbeddingMatrix getters/setters
dimnames<--method | LinearEmbeddingMatrix getters/setters
doesn't | Alternative Experiment methods
Dumping | Alternative Experiment methods

## -- F --

factorData | LinearEmbeddingMatrix getters/setters
factorData-method | LinearEmbeddingMatrix getters/setters
factorData<- | LinearEmbeddingMatrix getters/setters
factorData<--method | LinearEmbeddingMatrix getters/setters
featureLoadings | LinearEmbeddingMatrix getters/setters
featureLoadings-method | LinearEmbeddingMatrix getters/setters
featureLoadings<- | LinearEmbeddingMatrix getters/setters
featureLoadings<--method | LinearEmbeddingMatrix getters/setters

## -- H --

here, | Alternative Experiment methods

## -- I --

int_colData | Internal SingleCellExperiment functions
int_colData-method | Internal SingleCellExperiment functions
int_colData<- | Internal SingleCellExperiment functions
int_colData<--method | Internal SingleCellExperiment functions
int_elementMetadata | Internal SingleCellExperiment functions
int_elementMetadata-method | Internal SingleCellExperiment functions
int_elementMetadata<- | Internal SingleCellExperiment functions
int_elementMetadata<--method | Internal SingleCellExperiment functions
int_metadata | Internal SingleCellExperiment functions
int_metadata-method | Internal SingleCellExperiment functions
int_metadata<- | Internal SingleCellExperiment functions
int_metadata<--method | Internal SingleCellExperiment functions
isSpike | Defunct methods
isSpike<- | Defunct methods

## -- L --

length-method | Alternative Experiment methods
length-method | Row pair methods
LinearEmbeddingMatrix | LinearEmbeddingMatrix class
LinearEmbeddingMatrix-class | LinearEmbeddingMatrix class
logcounts | Named assay getters and setters
logcounts-method | Named assay getters and setters
logcounts<- | Named assay getters and setters
logcounts<--method | Named assay getters and setters

## -- M --

mainExpName | Alternative Experiment methods
mainExpName-method | Alternative Experiment methods
mainExpName<- | Alternative Experiment methods
mainExpName<--method | Alternative Experiment methods
methods | Alternative Experiment methods

## -- N --

names-method | Alternative Experiment methods
names<--method | Alternative Experiment methods
normcounts | Named assay getters and setters
normcounts-method | Named assay getters and setters
normcounts<- | Named assay getters and setters
normcounts<--method | Named assay getters and setters

## -- O --

objectVersion | Miscellaneous SingleCellExperiment methods
objectVersion-method | Miscellaneous SingleCellExperiment methods

## -- P --

parallel_slot_names-method | Internal SingleCellExperiment functions

## -- R --

rbind-method | LEM combining methods
rbind-method | Combining or subsetting SingleCellExperiment objects
rbind.reduced.dim.matrix | The reduced.dim.matrix class
reduced.dim.matrix | The reduced.dim.matrix class
reduced.dim.matrix-class | The reduced.dim.matrix class
reducedDim | Reduced dimensions methods
reducedDim-method | Reduced dimensions methods
reducedDim<- | Reduced dimensions methods
reducedDim<--method | Reduced dimensions methods
reducedDimNames | Reduced dimensions methods
reducedDimNames-method | Reduced dimensions methods
reducedDimNames<- | Reduced dimensions methods
reducedDimNames<--method | Reduced dimensions methods
reducedDims | Reduced dimensions methods
reducedDims-method | Reduced dimensions methods
reducedDims<- | Reduced dimensions methods
reducedDims<--method | Reduced dimensions methods
removeAltExps | Alternative Experiment methods
rowData-method | Internal SingleCellExperiment functions
rowPair | Row pair methods
rowPair-method | Row pair methods
rowPair<- | Row pair methods
rowPair<--method | Row pair methods
rowPairNames | Row pair methods
rowPairNames-method | Row pair methods
rowPairNames<- | Row pair methods
rowPairNames<--method | Row pair methods
rowPairs | Row pair methods
rowPairs-method | Row pair methods
rowPairs<- | Row pair methods
rowPairs<--method | Row pair methods
rowSubset | Get or set the row subset
rowSubset-method | Get or set the row subset
rowSubset<- | Get or set the row subset
rowSubset<--method | Get or set the row subset

## -- S --

sampleFactors | LinearEmbeddingMatrix getters/setters
sampleFactors-method | LinearEmbeddingMatrix getters/setters
sampleFactors<- | LinearEmbeddingMatrix getters/setters
sampleFactors<--method | LinearEmbeddingMatrix getters/setters
SCE-assays | Named assay getters and setters
SCE-combine | Combining or subsetting SingleCellExperiment objects
SCE-internals | Internal SingleCellExperiment functions
SCE-miscellaneous | Miscellaneous SingleCellExperiment methods
SEBC | Alternative Experiment methods
show-method | Miscellaneous LEM methods
show-method | Miscellaneous SingleCellExperiment methods
simplifyToSCE | Simplify a list to a single SingleCellExperiment
SingleCellExperiment | The SingleCellExperiment class
SingleCellExperiment-class | The SingleCellExperiment class
sizeFactorNames | Defunct methods
sizeFactors | Size factor methods
sizeFactors-method | Size factor methods
sizeFactors<--method | Size factor methods
so | Alternative Experiment methods
spikeNames | Defunct methods
splitAltExps | Split off alternative features
swapAltExp | Swap main and alternative Experiments

## -- T --

that | Alternative Experiment methods
the | Alternative Experiment methods
tpm | Named assay getters and setters
tpm-method | Named assay getters and setters
tpm<- | Named assay getters and setters
tpm<--method | Named assay getters and setters

## -- U --

unsplitAltExps | Unsplit the alternative experiments
updateObject | Update a SingleCellExperiment object
updateObject-method | Update a SingleCellExperiment object

## -- W --

weights | Named assay getters and setters
weights-method | Named assay getters and setters
weights<- | Named assay getters and setters
weights<--method | Named assay getters and setters

## -- misc --

$-method | LinearEmbeddingMatrix getters/setters
$<--method | LinearEmbeddingMatrix getters/setters
% | Alternative Experiment methods
[-method | LEM subsetting methods
[-method | Alternative Experiment methods
[-method | Combining or subsetting SingleCellExperiment objects
[-method | Row pair methods
[.reduced.dim.matrix | The reduced.dim.matrix class
[<--method | LEM subsetting methods
[<--method | Alternative Experiment methods
[<--method | Combining or subsetting SingleCellExperiment objects
[<--method | Row pair methods