Function reference • dreamlet

All functions

aggregateNonCountSignal(): Aggregation of single-cell signals

aggregateToPseudoBulk(): Aggregation of single-cell to pseudobulk data

aggregateVar(): Per-sample variance of single-cell counts

as.dreamletResult(): Convert list of regression fits to dreamletResult

assay(<dreamletResult>,<ANY>) assay(<dreamletProcessedData>,<ANY>) assay(<vpDF>,<ANY>): Get assay

assayNames(<dreamletResult>) assayNames(<dreamletProcessedData>) assayNames(<vpDF>): Get assayNames

buildClusterTreeFromPB(): Hierarchical clustering on cell types from pseudobulk

cellCounts(): Extract cell counts

cellSpecificityValues-class: Class cellSpecificityValues

cellTypeSpecificity(): Get cell type specificity of gene expression

checkFormula(): Check variables in a formula

coefNames(): Get coefficient names

colData(<dreamletProcessedData>): Extract colData from dreamletProcessedData

`colData<-`(<dreamletProcessedData>,<ANY>): Set colData

compositePosteriorTest(): Perform composite test on results from mashr

computeCellCounts(): Get cell counts with metadata

computeLogCPM(): Compute log normalized counts

computeNormCounts(): Compute normalized counts

details(): Extract details from dreamletProcessedData

diffVar(<dreamletResult>): Test differential variance

dreamlet(): Differential expression for each assay

dreamletCompareClusters(): Differential expression between pair of assays

dreamletProcessedData-class: Class dreamletProcessedData

dreamletResult-class: Class dreamletResult

dreamlet_mash_result-class: Class dreamlet_mash_result

dropRedundantTerms(): Drop redundant terms from the model

equalFormulas(): Check if two formulas are equal

`[`(<dreamletResult>,<ANY>,<ANY>,<ANY>) `[`(<dreamletProcessedData>,<ANY>,<ANY>,<ANY>): Subset with brackets

extractData(): Extract normalized expression and colData

fitVarPart(): Variance Partition analysis for each assay

getTreat(<dreamletResult>): Test if coefficient is different from a specified value

meta_analysis(): Meta-analysis across multiple studies

metadata(<dreamletProcessedData>): Extract metadata from dreamletProcessedData

outlier(): Multivariate outlier detection

outlierByAssay(): Outlier analysis for each assay

plotBeeswarm(): Beeswarm plot of effect sizes for each assay

plotCellComposition(): Bar plot of cell compositions

plotForest(): Forest plot

plotGeneHeatmap(): Heatmap of genes and assays

plotHeatmap(): Plot heatmap

plotPCA(<list>): Plot PCA of gene expression for an assay

plotPercentBars(<vpDF>) plotPercentBars(<cellSpecificityValues>): Bar plot of variance fractions

plotProjection(): Plot 2D projection

plotVarPart(<DataFrame>): Violin plot of variance fractions

plotViolin(): Plot Violins

plotVolcano(): Volcano plot for each cell type

plotVoom(): Plot voom curves from each cell type

print(<dreamletResult>) print(<dreamletProcessedData>): Print object

processAssays(): Processing SingleCellExperiment to dreamletProcessedData

processOneAssay(): Processing expression data from assay

removeConstantTerms(): Remove constant terms from formula

residuals(<dreamletResult>): Extract residuals from dreamletResult

run_mash(): Run mash analysis on dreamlet results

seeErrors(): Get error text

show(<dreamletResult>) show(<dreamletProcessedData>): Show object

sortCols(<vpDF>): Sort variance partition statistics

stackAssays(): Stack assays from pseudobulk

tabToMatrix(): Convert results table to matrix

topTable(<dreamletResult>): Table of Top Genes from dreamlet fit

vpDF-class: Class vpDF

zenith_gsa(<dreamletResult>,<GeneSetCollection>) zenith_gsa(<dreamlet_mash_result>,<GeneSetCollection>): Perform gene set analysis using zenith