# S4 Classes for Single Cell Data

## Documentation for package ‘SingleCellExperiment’ version 1.9.1

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

## Help Pages

A C D F H I L M N O 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
as.matrix-method | LinearEmbeddingMatrix getters/setters

## -- C --

c-method | Alternative Experiment methods
cbind-method | LEM combining methods
cbind-method | Combining or subsetting SingleCellExperiment objects
check | Alternative Experiment methods
clearSizeFactors | Size factors methods
clearSizeFactors-method | Size factors methods
clearSpikes | Spike-in methods
clearSpikes-method | Spike-in methods
coerce-method | The SingleCellExperiment class
colData-method | Internal SingleCellExperiment functions
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 --

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 | Spike-in methods
isSpike-method | Spike-in methods
isSpike<- | Spike-in methods
isSpike<--method | Spike-in methods

## -- L --

length-method | Alternative Experiment 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 --

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

## -- R --

rbind-method | LEM combining methods
rbind-method | Combining or subsetting SingleCellExperiment objects
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

## -- 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
SingleCellExperiment | The SingleCellExperiment class
SingleCellExperiment-class | The SingleCellExperiment class
sizeFactorNames | Size factors methods
sizeFactorNames-method | Size factors methods
sizeFactors | Size factors methods
sizeFactors-method | Size factors methods
sizeFactors<--method | Size factors methods
so | Alternative Experiment methods
spikeNames | Spike-in methods
spikeNames-method | Spike-in 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 --

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 | LEM subsetting methods
[<--method | Alternative Experiment methods
[<--method | Combining or subsetting SingleCellExperiment objects