All functions

DESeqAnalysis()

DESeq2 differential expression analysis

DESeqAnalysisList()

List containing related DESeq2 analyses

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

plotCounts(<DESeqAnalysis>)

Plot counts

plotDEGHeatmap(<DESeqResults>) plotDEGHeatmap(<DESeqAnalysis>)

Differentially expressed gene heatmap

plotDEGPCA(<DESeqResults>) plotDEGPCA(<DESeqAnalysis>)

Plot differentially expressed gene principal component analysis

plotMA(<DESeqResults>) plotMA(<DESeqAnalysis>)

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

plotVolcano(<DESeqResults>) plotVolcano(<DESeqAnalysis>)

Volcano plot

results(<DESeqDataSet>) results(<DESeqAnalysis>)

Results

resultsNames(<DESeqDataSet>) resultsNames(<DESeqAnalysis>)

Results names

resultsTables(<DESeqResults>) resultsTables(<DESeqAnalysis>)

Results tables

sampleData(<DESeqAnalysis>)

Sample data

show(<DESeqAnalysis>)

Show an object

topTables(<DESeqAnalysis>)

Top tables

updateObject(<DESeqAnalysis>)

Update an object to its current class definition