S4 Classes for Single Cell Data

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Documentation for package ‘SingleCellExperiment’ version 1.28.1

• 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