All functions

DESeqAnalysis()

DESeq2 differential expression analysis

DESeqAnalysisList()

List containing related DESeq2 analyses

alphaSummary()

Alpha level cutoff summary statistics

as

Force an object to belong to a class

contrastName()

Contrast name

contrastSamples()

Samples corresponding to a differential expression contrast

deg()

Differentially expressed genes

deseq

DESeq2 example analysis

export()

Export

lfcShrinkType()

Shrunken log2 fold change (LFC) type

markdown()

Markdown

plotCounts()

Plot counts

plotDEGHeatmap()

Differentially expressed gene heatmap

plotDEGPCA()

Plot differentially expressed gene principal component analysis

plotDEGUpset()

UpSet plot of directional DEG intersections across contrasts

plotMA()

MA-plot: plot differences versus averages for high-throughput data

plotPCA()

Principal component analysis plot

plotVolcano()

Volcano plot

results()

Results

resultsMatrix()

DESeqResults matrix

resultsNames()

Results names

resultsTables()

Results tables

sampleData()

Sample data

show(<DESeqAnalysis>)

Show an object

topTables()

Top tables

transformType()

Variance-stabilizing transformation type

updateObject(<DESeqAnalysis>)

Update an object to its current class definition