# S4 Classes for Single Cell Data

## Documentation for package ‘SingleCellExperiment’ version 1.2.0

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

## Help Pages

$-method | LinearEmbeddingMatrix getters/setters
$<--method | LinearEmbeddingMatrix getters/setters
as.matrix-method | LinearEmbeddingMatrix getters/setters
cbind-method | LEM combining methods
cbind-method | SCE combining methods
clearSizeFactors | Size factors methods
clearSizeFactors-method | Size factors methods
clearSpikes | Spike-in methods
clearSpikes-method | Spike-in methods
coerce-method | SingleCellExperiment class
colData-method | Miscellaneous SCE methods
counts | Named assay fields
counts-method | Named assay fields
counts<- | Named assay fields
counts<--method | Named assay fields
cpm | Named assay fields
cpm-method | Named assay fields
cpm<- | Named assay fields
cpm<--method | Named assay fields
dim-method | LinearEmbeddingMatrix getters/setters
dimnames-method | LinearEmbeddingMatrix getters/setters
dimnames<--method | LinearEmbeddingMatrix getters/setters
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
isSpike | Spike-in methods
isSpike-method | Spike-in methods
isSpike<- | Spike-in methods
isSpike<--method | Spike-in methods
LinearEmbeddingMatrix | LinearEmbeddingMatrix class
LinearEmbeddingMatrix-class | LinearEmbeddingMatrix class
logcounts | Named assay fields
logcounts-method | Named assay fields
logcounts<- | Named assay fields
logcounts<--method | Named assay fields
normcounts | Named assay fields
normcounts-method | Named assay fields
normcounts<- | Named assay fields
normcounts<--method | Named assay fields
objectVersion | Miscellaneous SCE methods
objectVersion-method | Miscellaneous SCE methods
rbind-method | LEM combining methods
rbind-method | SCE combining methods
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
reducedDims | Reduced dimensions methods
reducedDims-method | Reduced dimensions methods
reducedDims<- | Reduced dimensions methods
reducedDims<--method | Reduced dimensions methods
rowData-method | Miscellaneous SCE methods
sampleFactors | LinearEmbeddingMatrix getters/setters
sampleFactors-method | LinearEmbeddingMatrix getters/setters
sampleFactors<- | LinearEmbeddingMatrix getters/setters
sampleFactors<--method | LinearEmbeddingMatrix getters/setters
show-method | Miscellaneous LEM methods
show-method | Miscellaneous SCE methods
SingleCellExperiment | SingleCellExperiment class
SingleCellExperiment-class | 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
spikeNames | Spike-in methods
spikeNames-method | Spike-in methods
subset-method | SCE subsetting methods
tpm | Named assay fields
tpm-method | Named assay fields
tpm<- | Named assay fields
tpm<--method | Named assay fields
[-method | LEM subsetting methods
[-method | SCE subsetting methods
[<--method | LEM subsetting methods
[<--method | SCE subsetting methods