S4 Classes for Single Cell Data

[Up] [Top]

Documentation for package ‘SingleCellExperiment’ version 1.2.0

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