Test for Differential Exon Usage — testForDEU • DEXSeq

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(),
  fitType = c("DESeq2", "glmGamPoi")
)

Arguments

object: A DEXSeqDataSet object.
fullModel: The full model formula.
reducedModel: Null model formula.
BPPARAM: A "BiocParallelParam" instance. See ?bplapply for details.
fitType: Specifies what internal engine to use for fitting the GLMs. Options are "DESeq2" or "glmGamPoi".

Value

A DEXSeqDataSet with slots filled with information about the test.

Details

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

Examples


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