Inference of differential exon usage in RNA-Seq

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Documentation for package ‘DEXSeq’ version 1.8.0

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buildExonCountSet Makes an ExonCountSet object from R objects.
class:ExonCountSet "ExonCountSet", a container for exon count data
constructModelFrame Returns the model frame of an exonCountSet object for the GLM fits.
countReadsForDEXSeq Prepare annotation transcriptDb object for DEXSeq.
countReadsForDEXSeq-deprecated Prepare annotation transcriptDb object for DEXSeq.
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.
DEXSeq-deprecated This functions are deprecated and will become defunct.
DEXSeqHTML HTML report writer
doCompleteDEUAnalysis Perform complete differential exon usage analysis
estimateDispersions Estimate dispersions
estimateDispersions-method Estimate dispersions
estimateDispersions_BM Estimate exon dispersions, using the deprecated "big model" method
estimateExonDispersionsForModelFrame_BM Estimates exon dispersions for the (deprecated) "big model" method
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 "ExonCountSet", a container for exon count data
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_BM 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.
plotDispEsts Diagnostic plot for dispersion estimates and dispersion fit
plotDispEsts-method Diagnostic plot for dispersion estimates and dispersion fit
plotDispEsts-methods Diagnostic plot for dispersion estimates and dispersion fit
plotMA Generate an MA plot
plotMA-method Generate an MA plot
plotMA-methods Generate an MA plot
prepareAnnotationForDEXSeq Prepare annotation transcriptDb object for DEXSeq.
prepareAnnotationForDEXSeq-deprecated Prepare annotation transcriptDb object for DEXSeq.
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.
testForDEU_BM Test for Differential Exon Usage (with the old, deprecated "big model" approach.
testGeneForDEU_BM Test a single gene for differential exon usage using the old (and deprecated) "big model" approach.
[-method "ExonCountSet", a container for exon count data