Single-cell analysis toolkit for gene expression data in R


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Documentation for package ‘scater’ version 1.2.0

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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 --

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 --

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.
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
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
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
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 --

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
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.
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 --

writeSCESet Write an SCESet object to an HDF5 file

-- misc --

[-method Subsetting SCESet Objects