R: Test for Differential Exon Usage.

testForDEU {DEXSeq}

R Documentation

Test for Differential Exon Usage.

This will perform a likelihood ratio test for differential exon usage. Internally, it calls the DESeq2 function nbinomLRT.


  testForDEU( object, 
     fullModel = design(object), 
     reducedModel = ~ sample + exon, 
     BPPARAM=SerialParam() )

`object`	A DEXSeqDataSet object.
`fullModel`	The full model formula
`reducedModel`	Null model formula.
`BPPARAM`	A "BiocParallelParam" instance. See `?bplapply` for details.

The information of the variables of the formulas should be present in the colData of the DEXSeqDataSet object.

A DEXSeqDataSet with slots filled with information about the test.


  data(pasillaDEXSeqDataSet, package="pasilla")
  dxd <- estimateSizeFactors( dxd )
  dxd <- estimateDispersions( dxd )
  dxd <- testForDEU( dxd )

[Package DEXSeq version 1.28.3 Index]