# Single-cell analysis toolkit for gene expression data in R

## Documentation for package ‘scater’ version 1.4.0

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

## Help Pages

A B C F G I M N P R S T U W misc

scater-package | Single-cell analysis toolkit for expression in R

## -- A --

areSizeFactorsCentred | Check if the size factors are centred at unity
arrange | Arrange rows of 'pData(object)' by variables.
arrange-method | Arrange rows of 'pData(object)' by variables.
arrange.SCESet | Arrange rows of 'pData(object)' by variables.

## -- B --

bootstraps | Accessor and replacement for bootstrap results in an SCESet object
bootstraps-method | Accessor and replacement for bootstrap results in an SCESet object
bootstraps.SCESet | Accessor and replacement for bootstrap results in an SCESet object
bootstraps<- | Accessor and replacement for bootstrap results in an SCESet object
bootstraps<--method | Accessor and replacement for bootstrap results in an SCESet object

## -- C --

calcAverage | Calculate average counts, adjusting for size factors or library size
calcIsExprs | Calculate which features are expressed in which cells using a threshold on observed counts, transcripts-per-million, counts-per-million, FPKM, or defined expression levels.
calculateCPM | Calculate counts per million (CPM)
calculateFPKM | Calculate fragments per kilobase of exon per million reads mapped (FPKM)
calculateQCMetrics | Calculate QC metrics
calculateTPM | Calculate transcripts-per-million (TPM)
cellDist | cellPairwiseDistances in an SCESet object
cellDist-method | cellPairwiseDistances in an SCESet object
cellDist<- | cellPairwiseDistances in an SCESet object
cellDist<--method | cellPairwiseDistances in an SCESet object
cellDistSCESet | cellPairwiseDistances in an SCESet object
cellNames | Get or set cell names from an SCESet object
cellNames<- | Get or set cell names from an SCESet object
cellNames<--method | Get or set cell names from an SCESet object
cellPairwiseDistances | cellPairwiseDistances in an SCESet object
cellPairwiseDistances-method | cellPairwiseDistances in an SCESet object
cellPairwiseDistances.SCESet | cellPairwiseDistances in an SCESet object
cellPairwiseDistances<- | cellPairwiseDistances in an SCESet object
cellPairwiseDistances<--method | cellPairwiseDistances in an SCESet object
counts | Accessors for the 'counts' element of an SCESet object.
counts-method | Accessors for the 'counts' element of an SCESet object.
counts.SCESet | Accessors for the 'counts' element of an SCESet object.
counts<--method | Accessors for the 'counts' element of an SCESet object.
cpm | Accessors for the 'cpm' (counts per million) element of an SCESet object.
cpm-method | Accessors for the 'cpm' (counts per million) element of an SCESet object.
cpm<- | Accessors for the 'cpm' (counts per million) element of an SCESet object.
cpm<--method | Accessors for the 'cpm' (counts per million) element of an SCESet object.
cpmSCESet | Accessors for the 'cpm' (counts per million) element of an SCESet object.

## -- F --

fData | Replaces featureData in an SCESet object
fData-method | Replaces featureData in an SCESet object
fData<--method | Replaces featureData in an SCESet object
featDist | featurePairwiseDistances in an SCESet object
featDist-method | featurePairwiseDistances in an SCESet object
featDist<- | featurePairwiseDistances in an SCESet object
featDist<--method | featurePairwiseDistances in an SCESet object
featDistSCESet | featurePairwiseDistances in an SCESet object
featureControlInfo | featureControlInfo in an SCESet object
featureControlInfo-method | featureControlInfo in an SCESet object
featureControlInfo.SCESet | featureControlInfo in an SCESet object
featureControlInfo<- | featureControlInfo in an SCESet object
featureControlInfo<--method | featureControlInfo in an SCESet object
featurePairwiseDistances | featurePairwiseDistances in an SCESet object
featurePairwiseDistances-method | featurePairwiseDistances in an SCESet object
featurePairwiseDistances<- | featurePairwiseDistances in an SCESet object
featurePairwiseDistances<--method | featurePairwiseDistances in an SCESet object
featurePairwiseDistancesSCESet | featurePairwiseDistances in an SCESet object
filter | Return 'SCESet' with cells matching conditions.
filter-method | Return 'SCESet' with cells matching conditions.
filter.SCESet | Return 'SCESet' with cells matching conditions.
findImportantPCs | Find most important principal components for a given variable
fpkm | Accessors for the 'fpkm' (fragments per kilobase of exon per million reads mapped) element of an SCESet object.
fpkm-method | Accessors for the 'fpkm' (fragments per kilobase of exon per million reads mapped) element of an SCESet object.
fpkm.SCESet | Accessors for the 'fpkm' (fragments per kilobase of exon per million reads mapped) element of an SCESet object.
fpkm<- | Accessors for the 'fpkm' (fragments per kilobase of exon per million reads mapped) element of an SCESet object.
fpkm<--method | Accessors for the 'fpkm' (fragments per kilobase of exon per million reads mapped) element of an SCESet object.
fromCellDataSet | Convert a 'CellDataSet' to an 'SCESet'

## -- G --

getBMFeatureAnnos | Get feature annotation information from Biomart
getExprs | Retrieve a representation of gene expression
get_exprs | Generic accessor for expression data from an SCESet object.
get_exprs-method | Generic accessor for expression data from an SCESet object.
get_exprs.SCESet | Generic accessor for expression data from an SCESet object.

## -- I --

isOutlier | Identify if a cell is an outlier based on a metric
isSpike | Get spike-in features in an SCESet object
isSpike-method | Get spike-in features in an SCESet object
is_exprs | Accessors for the 'is_exprs' element of an SCESet object.
is_exprs-method | Accessors for the 'is_exprs' element of an SCESet object.
is_exprs.SCESet | Accessors for the 'is_exprs' element of an SCESet object.
is_exprs<- | Accessors for the 'is_exprs' element of an SCESet object.
is_exprs<--method | Accessors for the 'is_exprs' element of an SCESet object.

## -- M --

mergeSCESet | Merge SCESet objects
multiplot | Multiple plot function for ggplot2 plots
mutate | Add new variables to 'pData(object)'.
mutate-method | Add new variables to 'pData(object)'.
mutate.SCESet | Add new variables to 'pData(object)'.

## -- N --

newSCESet | Create a new SCESet object.
nexprs | Count the number of expressed genes per cell
normalise | Normalise an SCESet object using pre-computed size factors
normalise-method | Normalise an SCESet object using pre-computed size factors
normaliseExprs | Normalise expression expression levels for an SCESet object
normalize | Normalise an SCESet object using pre-computed size factors
normalize-method | Normalise an SCESet object using pre-computed size factors
normalize.SCESet | Normalise an SCESet object using pre-computed size factors
normalizeExprs | Normalise expression expression levels for an SCESet object
normliseExprs | Normalise expression expression levels for an SCESet object
norm_counts | Accessors for the 'norm_counts' element of an SCESet object.
norm_counts-method | Accessors for the 'norm_counts' element of an SCESet object.
norm_counts.SCESet | Accessors for the 'norm_counts' element of an SCESet object.
norm_counts<- | Accessors for the 'norm_counts' element of an SCESet object.
norm_counts<--method | Accessors for the 'norm_counts' element of an SCESet object.
norm_cpm | Accessors for the 'norm_cpm' (normalised counts per million) element of an SCESet object.
norm_cpm-method | Accessors for the 'norm_cpm' (normalised counts per million) element of an SCESet object.
norm_cpm.SCESet | Accessors for the 'norm_cpm' (normalised counts per million) element of an SCESet object.
norm_cpm<- | Accessors for the 'norm_cpm' (normalised counts per million) element of an SCESet object.
norm_cpm<--method | Accessors for the 'norm_cpm' (normalised counts per million) element of an SCESet object.
norm_exprs | Accessors for the 'norm_exprs' (normalised expression) element of an SCESet object.
norm_exprs-method | Accessors for the 'norm_exprs' (normalised expression) element of an SCESet object.
norm_exprs.SCESet | Accessors for the 'norm_exprs' (normalised expression) element of an SCESet object.
norm_exprs<- | Accessors for the 'norm_exprs' (normalised expression) element of an SCESet object.
norm_exprs<--method | Accessors for the 'norm_exprs' (normalised expression) element of an SCESet object.
norm_fpkm | Accessors for the 'norm_fpkm' (normalised fragments per kilobase of exon per million reads mapped) element of an SCESet object.
norm_fpkm-method | Accessors for the 'norm_fpkm' (normalised fragments per kilobase of exon per million reads mapped) element of an SCESet object.
norm_fpkm.SCESet | Accessors for the 'norm_fpkm' (normalised fragments per kilobase of exon per million reads mapped) element of an SCESet object.
norm_fpkm<- | Accessors for the 'norm_fpkm' (normalised fragments per kilobase of exon per million reads mapped) element of an SCESet object.
norm_fpkm<--method | Accessors for the 'norm_fpkm' (normalised fragments per kilobase of exon per million reads mapped) element of an SCESet object.
norm_tpm | Accessors for the 'norm_tpm' (transcripts per million) element of an SCESet object.
norm_tpm-method | Accessors for the 'norm_tpm' (transcripts per million) element of an SCESet object.
norm_tpm.SCESet | Accessors for the 'norm_tpm' (transcripts per million) element of an SCESet object.
norm_tpm<- | Accessors for the 'norm_tpm' (transcripts per million) element of an SCESet object.
norm_tpm<--method | Accessors for the 'norm_tpm' (transcripts per million) element of an SCESet object.

## -- P --

pData | Replaces phenoData in an SCESet object
pData-method | Replaces phenoData in an SCESet object
pData<--method | Replaces phenoData in an SCESet object
plot | Plot an overview of expression for each cell
plot-method | Plot an overview of expression for each cell
plotDiffusionMap | Plot a diffusion map for an SCESet object
plotDiffusionMap-method | Plot a diffusion map for an SCESet object
plotDiffusionMapSCESet | Plot a diffusion map for an SCESet object
plotExplanatoryVariables | Plot explanatory variables ordered by percentage of phenotypic variance explained
plotExpression | Plot expression values for a set of features (e.g. genes or transcripts)
plotExpression-method | Plot expression values for a set of features (e.g. genes or transcripts)
plotExpressionDefault | Plot expression values for a set of features (e.g. genes or transcripts)
plotExpressionSCESet | Plot expression values for a set of features (e.g. genes or transcripts)
plotExprsFreqVsMean | Plot frequency of expression against mean expression level
plotExprsVsTxLength | Plot expression against transcript length
plotFeatureData | Plot feature (gene) data from an SCESet object
plotHighestExprs | Plot the features with the highest expression values
plotMDS | Produce a multidimensional scaling plot for an SCESet object
plotMDS-method | Produce a multidimensional scaling plot for an SCESet object
plotMDSSCESet | Produce a multidimensional scaling plot for an SCESet object
plotMetadata | Plot metadata for cells or features
plotPCA | Plot PCA for an SCESet object
plotPCA-method | Plot PCA for an SCESet object
plotPCASCESet | Plot PCA for an SCESet object
plotPhenoData | Plot phenotype data from an SCESet object
plotPlatePosition | Plot cells in plate positions
plotQC | Produce QC diagnostic plots
plotReducedDIm | Plot reduced dimension representation of cells
plotReducedDim | Plot reduced dimension representation of cells
plotReducedDim-method | Plot reduced dimension representation of cells
plotReducedDim.default | Plot reduced dimension representation of cells
plotReducedDim.SCESet | Plot reduced dimension representation of cells
plotRLE | Plot a relative log expression (RLE) plot
plotRLE-method | Plot a relative log expression (RLE) plot
plotSCESet | Plot an overview of expression for each cell
plotTSNE | Plot t-SNE for an SCESet object
plotTSNE-method | Plot t-SNE for an SCESet object

## -- R --

read10XResults | Load in data from 10X experiment
readKallistoResults | Read kallisto results from a batch of jobs
readKallistoResultsOneSample | Read kallisto results for a single sample into a list
readSalmonResults | Read Salmon results from a batch of jobs
readSalmonResultsOneSample | Read Salmon results for a single sample into a list
readTxResults | Read transcript quantification data with tximport package
redDim | Reduced dimension representation for cells in an SCESet object
redDim-method | Reduced dimension representation for cells in an SCESet object
redDim.SCESet | Reduced dimension representation for cells in an SCESet object
redDim<- | Reduced dimension representation for cells in an SCESet object
redDim<--method | Reduced dimension representation for cells in an SCESet object
reducedDimension | Reduced dimension representation for cells in an SCESet object
reducedDimension-method | Reduced dimension representation for cells in an SCESet object
reducedDimension.SCESet | Reduced dimension representation for cells in an SCESet object
reducedDimension<- | Reduced dimension representation for cells in an SCESet object
reducedDimension<--method | Reduced dimension representation for cells in an SCESet object
rename | Rename variables of 'pData(object)'.
rename-method | Rename variables of 'pData(object)'.
rename.SCESet | Rename variables of 'pData(object)'.
runKallisto | Run kallisto on FASTQ files to quantify feature abundance
runSalmon | Run Salmon on FASTQ files to quantify feature abundance

## -- S --

scater_gui | scater GUI function
SCESet | The "Single Cell Expression Set" (SCESet) class
SCESet-class | The "Single Cell Expression Set" (SCESet) class
SCESet-subset | Subsetting SCESet Objects
sc_example_cell_info | Cell information for the small example single-cell counts dataset to demonstrate capabilities of scater
sc_example_counts | A small example of single-cell counts dataset to demonstrate capabilities of scater
setSpike | Set spike-in features in an SCESet object
setSpike<- | Set spike-in features in an SCESet object
setSpike<--method | Set spike-in features in an SCESet object
set_exprs | Assignment method for the new elements of an SCESet object.
set_exprs<- | Assignment method for the new elements of an SCESet object.
set_exprs<--method | Assignment method for the new elements of an SCESet object.
sizeFactors | Accessors size factors of an SCESet object.
sizeFactors-method | Accessors size factors of an SCESet object.
sizeFactors.SCESet | Accessors size factors of an SCESet object.
sizeFactors<- | Accessors size factors of an SCESet object.
sizeFactors<--method | Accessors size factors of an SCESet object.
spikes | Extract expression values for spike-in features in an SCESet object
spikes-method | Extract expression values for spike-in features in an SCESet object
stand_exprs | Accessors for the 'stand_exprs' (standardised expression) element of an SCESet object.
stand_exprs-method | Accessors for the 'stand_exprs' (standardised expression) element of an SCESet object.
stand_exprs.SCESet | Accessors for the 'stand_exprs' (standardised expression) element of an SCESet object.
stand_exprs<- | Accessors for the 'stand_exprs' (standardised expression) element of an SCESet object.
stand_exprs<--method | Accessors for the 'stand_exprs' (standardised expression) element of an SCESet object.
summariseExprsAcrossFeatures | Summarise expression values across feature

## -- T --

toCellDataSet | Convert an 'SCESet' to a 'CellDataSet'
tpm | Accessors for the 'tpm' (transcripts per million) element of an SCESet object.
tpm-method | Accessors for the 'tpm' (transcripts per million) element of an SCESet object.
tpm.SCESet | Accessors for the 'tpm' (transcripts per million) element of an SCESet object.
tpm<- | Accessors for the 'tpm' (transcripts per million) element of an SCESet object.
tpm<--method | Accessors for the 'tpm' (transcripts per million) element of an SCESet object.

## -- U --

updateSCESet | Update an SCESet object to the current version

## -- W --

whichSpike | Identify spike-in feature control sets in an SCESet object
whichSpike-method | Identify spike-in feature control sets in an SCESet object
writeSCESet | Write an SCESet object to an HDF5 file

## -- misc --

[-method | Subsetting SCESet Objects