S4 Classes for Single Cell Data

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Documentation for package ‘SingleCellExperiment’ version 1.10.1

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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 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
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
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 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 --

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