testForDEU: Test for Differential Exon Usage.

In DEXSeq: Inference of differential exon usage in RNA-Seq

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 )

DEXSeq documentation built on Nov. 8, 2020, 5:11 p.m.