Inference of differential exon usage in RNA-Seq

[Up] [Top]

Documentation for package ‘DEXSeq’ version 1.0.2

Help Pages

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
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.