Inference of differential exon usage in RNA-Seq


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Documentation for package ‘DEXSeq’ version 1.4.0

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counts Accessors for the 'counts' slot of a ExonCountSet object.
counts-method Accessors for the 'counts' slot of a ExonCountSet object.
counts<--method Accessors for the 'counts' slot of a ExonCountSet object.
countTableForGene Count table for a given geneID.
design Accessor function for the design annotation from a ExonCountSet object.
design-method Accessor function for the design annotation from a ExonCountSet object.
design<--method Accessor function for the design annotation from a ExonCountSet object.
DEUresultTable Get a result table from the analysis workflow.
DEXSeqHTML HTML report writer
estimateDispersions Estimate exon dispersions
estimateDispersions-method Estimate exon dispersions
estimateExonDispersionsForModelFrame Estimates exon dispersions
estimatelog2FoldChanges Fold changes (log2) from the fitted expression values in the GLM.
estimateSizeFactors Estimate the size factors for an ExonCountSet
estimateSizeFactors-method Estimate the size factors for an ExonCountSet
ExonCountSet-class "ExonCountSet", a container for exon count data
exonIDs Accessor for the exonIDs in an ExonCountSet object.
exonIDs<- Accessor for the exonIDs in an ExonCountSet object.
fitDispersionFunction Fit the mean-variance function.
geneCountTable Makes a count table for genes.
geneIDs Accessor for the geneIDs in an ExonCountSet object.
geneIDs<- Accessor for the geneIDs in an ExonCountSet object.
makeCompleteDEUAnalysis Complete differential exon usage analysis
modelFrameForGene Makes the model frame for a geneID.
newExonCountSet Creates an ExonCountSet object
perGeneQValue Summarize per-exon p-values into per-gene q-values.
plotDEXSeq Visualization of the fitted expression, fitted splicing or the normalized counts.
read.HTSeqCounts Read counts output from HTSeq script.
sizeFactors Accessor functions for the sizeFactors information in a ExonCountSet
sizeFactors-method Accessor functions for the sizeFactors information in a ExonCountSet
sizeFactors<--method Accessor functions for the sizeFactors information in a ExonCountSet
subsetByGenes Making an ExonCountSet object from another one with a subset of its genes.
testForDEU Test for Differential Exon Usage.
testGeneForDEU Test a single gene for differential exon usage.