All functions

DESeqAnalysis()

DESeq2 differential expression analysis

alphaSummary(<DESeqDataSet>)

Alpha level cutoff summary statistics

as

Force an object to belong to a class

contrastName(<DESeqResults>) contrastName(<DESeqAnalysis>)

Contrast name

contrastSamples(<DESeqAnalysis>)

Samples corresponding to a differential expression contrast

deg(<DESeqResults>) deg(<DESeqAnalysis>)

Differentially expressed genes

deseq

DESeq2 example analysis

export(<DESeqAnalysis>)

Export

markdown(<DESeqAnalysis>)

Markdown

plotDEGHeatmap(<DESeqAnalysis>)

Differentially expressed gene heatmap

plotDEGPCA(<DESeqAnalysis>)

Plot differentially expressed gene principal component analysis

plotGene(<DESeqAnalysis>)

Plot gene expression

plotMA(<DESeqAnalysis>)

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

plotVolcano(<DESeqAnalysis>)

Volcano plot

resultsTables(<DESeqAnalysis>)

Results tables

show(<DESeqAnalysis>)

Show an object

topTables(<DESeqAnalysis>)

Top tables of differentially expressed genes