SCESet                  The "Single Cell Expression Set" (SCESet) class
SCESet-subset           Subsetting SCESet Objects
areSizeFactorsCentred   Check if the size factors are centred at unity
arrange                 Arrange rows of 'pData(object)' by variables.
bootstraps              Accessor and replacement for bootstrap results
                        in an SCESet object
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)
cellNames<-             Get or set cell names from an SCESet object
cellPairwiseDistances   cellPairwiseDistances in an SCESet object
counts                  Accessors for the 'counts' element of an SCESet
                        object.
cpm                     Accessors for the 'cpm' (counts per million)
                        element of an SCESet object.
fData<-,SCESet,AnnotatedDataFrame-method
                        Replaces featureData in an SCESet object
featureControlInfo      featureControlInfo in an SCESet object
featurePairwiseDistances
                        featurePairwiseDistances in an SCESet object
filter                  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.
fromCellDataSet         Convert a 'CellDataSet' to an 'SCESet'
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.
isOutlier               Identify if a cell is an outlier based on a
                        metric
isSpike                 Get spike-in features in an SCESet object
is_exprs                Accessors for the 'is_exprs' element of an
                        SCESet object.
mergeSCESet             Merge SCESet objects
multiplot               Multiple plot function for ggplot2 plots
mutate                  Add new variables to 'pData(object)'.
newSCESet               Create a new SCESet object.
nexprs                  Count the number of expressed genes per cell
norm_counts             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_exprs              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_tpm                Accessors for the 'norm_tpm' (transcripts per
                        million) element of an SCESet object.
normaliseExprs          Normalise expression expression levels for an
                        SCESet object
normalize               Normalise an SCESet object using pre-computed
                        size factors
pData<-,SCESet,AnnotatedDataFrame-method
                        Replaces phenoData in an SCESet object
plot                    Plot an overview of expression for each cell
plotDiffusionMap        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)
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
plotMetadata            Plot metadata for cells or features
plotPCA                 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
plotRLE                 Plot a relative log expression (RLE) plot
plotReducedDim          Plot reduced dimension representation of cells
plotTSNE                Plot t-SNE for an SCESet object
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
reducedDimension        Reduced dimension representation for cells in
                        an SCESet object
rename                  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
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
scater-package          Single-cell analysis toolkit for expression in
                        R
scater_gui              scater GUI function
setSpike                Set spike-in features in an SCESet object
set_exprs<-             Assignment method for the new elements of an
                        SCESet object.
sizeFactors             Accessors size factors of an SCESet object.
spikes                  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.
summariseExprsAcrossFeatures
                        Summarise expression values across feature
toCellDataSet           Convert an 'SCESet' to a 'CellDataSet'
tpm                     Accessors for the 'tpm' (transcripts per
                        million) element of an SCESet object.
updateSCESet            Update an SCESet object to the current version
whichSpike              Identify spike-in feature control sets in an
                        SCESet object
writeSCESet             Write an SCESet object to an HDF5 file
