testForDEU: Test for Differential Exon Usage

In areyesq89/DEXSeq: Inference of differential exon usage in RNA-Seq

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(),
  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".

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 )

areyesq89/DEXSeq documentation built on Oct. 15, 2023, 1:40 p.m.