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 alphaThreshold,DESeqAnalysis-method alphaThreshold,DESeqAnalysisList-method alphaThreshold,DESeqResults-method alphaThreshold,DESeqResultsList-method alphaThreshold alphaThreshold alphaThreshold alphaThreshold alphaThreshold alphaThreshold alphaThreshold: Alpha threshold

apeglmResults(): Run a quick pairwise contrast using lfcShrink with apeglm

baseMeanThreshold baseMeanThreshold baseMeanThreshold,DESeqAnalysis-method baseMeanThreshold,DESeqAnalysisList-method baseMeanThreshold,DESeqResults-method baseMeanThreshold,DESeqResultsList-method baseMeanThreshold baseMeanThreshold baseMeanThreshold baseMeanThreshold baseMeanThreshold baseMeanThreshold baseMeanThreshold baseMeanThreshold: Base mean threshold

as.DESeqDataSet() as.DESeqTransform(): Coercion methods

combine(): Combine multiple objects

contrastName() `contrastName<-`(): Contrast name

contrastSamples(): Samples corresponding to a differential expression contrast

correlation(): Correlation

deg(): Differentially expressed genes

degIntersection(): Intersection of differentially expressed genes

degPerContrast(): Base mean threshold

deseq: DESeq2 example analysis

deseqMinimal: Minimal 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 interestingGroups,DESeqAnalysis-method interestingGroups interestingGroups: Interesting groups

lfcShrink() `lfcShrink<-`(): Shrink log2 fold changes

lfcShrinkType(): Shrunken log2 fold change (LFC) type

lfcThreshold lfcThreshold lfcThreshold,DESeqAnalysis-method lfcThreshold,DESeqAnalysisList-method lfcThreshold,DESeqResults-method lfcThreshold,DESeqResultsList-method lfcThreshold lfcThreshold lfcThreshold lfcThreshold lfcThreshold lfcThreshold: Log2 fold change threshold

markdownTables(): Markdown tables

matchMetadataToFiles(): Match user metadata to file names used for tximport

plotBaseMean(): Plot base mean distribution

plotContrastScatter(): Plot scatterplot of differential expression contrast

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

plotCorrelationHeatmap() plotHeatmap() plotQuantileHeatmap(): Heatmap

plotLFC(): Plot log2 fold change distributions

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

transformType(): Variance-stabilizing transformation type

updateObject(): Update object