Function reference • DESeqAnalysis

All functions
`DESeqAnalysis-class`	DESeq2 differential expression analysis
`DESeqAnalysis()`	DESeq2 differential expression analysis
`DESeqAnalysisList-class`	List containing related DESeq2 analyses
`DESeqAnalysisList()`	List containing related DESeq2 analyses
`DESeqResultsList-class`	List containing related DESeqResults objects
`DESeqResultsList()`	List containing related DESeqResults objects
`alphaSummary()`	Alpha level cutoff summary statistics
`alphaThreshold()` `alphaThreshold<-`()	Alpha threshold
`apeglmResults()`	Run a quick pairwise contrast using lfcShrink with apeglm
`as`	Force an object to belong to a class
`baseMeanThreshold()` `baseMeanThreshold<-`()	Base mean threshold
`combine()`	Combine multiple objects
`contrastName()` `contrastName<-`()	Contrast name
`contrastSamples()`	Samples corresponding to a differential expression contrast
`correlation()`	Correlation
`dds_list`	List of DESeqDataSet example objects
`deg()`	Differentially expressed genes
`degIntersection()`	Intersection of differentially expressed genes
`degPerContrast()`	Base mean threshold
`deseq`	DESeq2 example analysis
`export()`	Export
`[`(<DESeqAnalysis>,<ANY>,<ANY>,<ANY>)	Extract or replace parts of an object
`importPairwiseContrasts()`	Import pairwise contrasts from a file
`interestingGroups()` `interestingGroups<-`()	Interesting groups
`lfcShrink()` `lfcShrink<-`()	Shrink log2 fold changes
`lfcShrinkType()`	Shrunken log2 fold change (LFC) type
`lfcThreshold()` `lfcThreshold<-`()	Log2 fold change threshold
`matchMetadataToFiles()`	Match user metadata to file names used for tximport
`plotBaseMean()`	Plot base mean distribution
`plotCounts()`	Plot counts
`plotDEGHeatmap()`	Differentially expressed gene heatmap
`plotDEGPCA()`	Plot differentially expressed gene principal component analysis
`plotDEGStackedBar()`	Stacked bar plot of DEGs
`plotDEGUpset()`	UpSet plot of directional DEG intersections across contrasts
`plotHeatmap()` `plotCorrelationHeatmap()` `plotQuantileHeatmap()`	Heatmap
`plotMA()`	MA plot
`plotPCA()`	Principal component analysis plot
`plotVolcano()`	Volcano plot
`prepareTximportFiles()`	Prepare quant files for tximport
`results()`	Results
`resultsDiff()`	Relative difference of results
`resultsMatrix()`	DESeq aggregate results matrix
`resultsNames()` `resultsNames<-`()	Results names
`resultsTables()`	Results tables
`sampleData()`	Sample data
`show()`	Show an object
`topTables()`	Top tables
`transformType()`	Variance-stabilizing transformation type
`updateObject()`	Update object

Reference

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