Acid Genomics DESeq2 Analysis Utilities

Documentation for package ‘DESeqAnalysis’ version 0.6.8

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-- A --

alphaSummary	Alpha level cutoff summary statistics
alphaSummary-method	Alpha level cutoff summary statistics
alphaThreshold	Alpha threshold
alphaThreshold-method	Alpha threshold
alphaThreshold<-	Alpha threshold
alphaThreshold<--method	Alpha threshold
apeglmResults	Run a quick pairwise contrast using lfcShrink with apeglm
apeglmResults-method	Run a quick pairwise contrast using lfcShrink with apeglm
as.DESeqDataSet	Coercion methods
as.DESeqDataSet-method	Coercion methods
as.DESeqTransform	Coercion methods
as.DESeqTransform-method	Coercion methods

-- B --

-- C --

coerce	Coercion methods
coerce-method	Coercion methods
combine	Combine multiple objects
combine-method	Combine multiple objects
contrastName	Contrast name
contrastName-method	Contrast name
contrastName<-	Contrast name
contrastName<--method	Contrast name
contrastSamples	Samples corresponding to a differential expression contrast
contrastSamples-method	Samples corresponding to a differential expression contrast
correlation	Correlation
correlation-method	Correlation

-- D --

deg	Differentially expressed genes
deg-method	Differentially expressed genes
degIntersection	Intersection of differentially expressed genes
degIntersection-method	Intersection of differentially expressed genes
degPerContrast	Base mean threshold
degPerContrast-method	Base mean threshold
deseq	DESeq2 example analysis
DESeqAnalysis	DESeq2 differential expression analysis
DESeqAnalysis-class	DESeq2 differential expression analysis
DESeqAnalysisList	List containing related DESeq2 analyses
DESeqAnalysisList-class	List containing related DESeq2 analyses
DESeqAnalysisList-method	List containing related DESeq2 analyses
deseqMinimal	Minimal DESeq2 example analysis
DESeqResultsList	List containing related DESeqResults objects
DESeqResultsList-class	List containing related DESeqResults objects
DESeqResultsList-method	List containing related DESeqResults objects

-- E --

export	Export
export-method	Export
extract	Extract or replace parts of an object

-- I --

importPairwiseContrasts	Import pairwise contrasts from a file
interestingGroups	Interesting groups
interestingGroups-method	Interesting groups
interestingGroups<-	Interesting groups
interestingGroups<--method	Interesting groups

-- L --

lfcShrink	Shrink log2 fold changes
lfcShrink-method	Shrink log2 fold changes
lfcShrink<-	Shrink log2 fold changes
lfcShrink<--method	Shrink log2 fold changes
lfcShrinkType	Shrunken log2 fold change (LFC) type
lfcShrinkType-method	Shrunken log2 fold change (LFC) type
lfcThreshold	Log2 fold change threshold
lfcThreshold-method	Log2 fold change threshold
lfcThreshold<-	Log2 fold change threshold
lfcThreshold<--method	Log2 fold change threshold

-- M --

markdownTables	Markdown tables
markdownTables-method	Markdown tables

-- P --

plotBaseMean	Plot base mean distribution
plotBaseMean-method	Plot base mean distribution
plotContrastScatter	Plot scatterplot of differential expression contrast
plotContrastScatter-method	Plot scatterplot of differential expression contrast
plotCorrelationHeatmap	Heatmap
plotCorrelationHeatmap-method	Heatmap
plotCounts	Plot counts
plotCounts-method	Plot counts
plotDEGHeatmap	Differentially expressed gene heatmap
plotDEGHeatmap-method	Differentially expressed gene heatmap
plotDEGPCA	Plot differentially expressed gene principal component analysis
plotDEGPCA-method	Plot differentially expressed gene principal component analysis
plotDEGStackedBar	Stacked bar plot of DEGs
plotDEGStackedBar-method	Stacked bar plot of DEGs
plotDEGUpset	UpSet plot of directional DEG intersections across contrasts
plotDEGUpset-method	UpSet plot of directional DEG intersections across contrasts
plotHeatmap	Heatmap
plotHeatmap-method	Heatmap
plotLFC	Plot log2 fold change distributions
plotLFC-method	Plot log2 fold change distributions
plotMA	MA plot
plotMA-method	MA plot
plotPCA	Principal component analysis plot
plotPCA-method	Principal component analysis plot
plotQuantileHeatmap	Heatmap
plotQuantileHeatmap-method	Heatmap
plotVolcano	Volcano plot
plotVolcano-method	Volcano plot
prepareTximportFiles	Prepare quant files for tximport

-- R --

results	Results
results-method	Results
resultsDiff	Relative difference of results
resultsDiff-method	Relative difference of results
resultsMatrix	DESeq aggregate results matrix
resultsMatrix-method	DESeq aggregate results matrix
resultsNames	Results names
resultsNames-method	Results names
resultsNames<-	Results names
resultsNames<--method	Results names
resultsTables	Results tables
resultsTables-method	Results tables

-- S --

-- T --

transformType	Variance-stabilizing transformation type
transformType-method	Variance-stabilizing transformation type

-- U --

updateObject	Update object
updateObject-method	Update object

-- misc --

Extract or replace parts of an object