testForDEU: Test for Differential Exon Usage.

Description Usage Arguments Details Value Examples

View source: R/core.R

Description

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

Usage

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  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

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

areyesq89/DEXSeq documentation built on June 26, 2020, 2:31 a.m.