testForDEU {DEXSeq}R Documentation

Test for Differential Exon Usage.

Description

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

Usage


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

Arguments

object

A DEXSeqDataSet object.

fullModel

The full model formula

reducedModel

Null model formula.

BPPARAM

A "BiocParallelParam" instance. See ?bplapply for details.

Details

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

Value

A DEXSeqDataSet with slots filled with information about the test.

Examples


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


[Package DEXSeq version 1.26.0 Index]