testForDEU {DEXSeq}R Documentation

Test for Differential Exon Usage.

Description

This function tests for differential exon usage for each of the exons in the object. It stores the results in the fields fData(ecs)$pvalue and fData(ecs)$padjust.

Usage

testForDEU( ecs, 
   formula0 = ~ sample + exon, 
   formula1 = ~ sample + exon + condition : exon, 
   dispColumn="dispersion", nCores = 1 )

Arguments

ecs

An ExonCountSet object.

formula0

Formula for the null model to be used in the GLM fit.

formula1

Formula for the full model to be used in the GLM fit.

dispColumn

Column name from the feature data frame from where to take the dispersions.

nCores

Number of CPUcores to be used to calculate the $p$-values. The parallel package must be loaded to use more than 1 core.

Details

The terms in the formulas must be columns of design(ecs).

Value

An ExonCountSet object with fData(ecs)$pvalue and fData(ecs)$padjust data slots filled.

Examples

     ## Not run: 
        data("pasillaExons", package="pasilla")
        pasillaExons <- estimateSizeFactors( pasillaExons )
        pasillaExons <- estimateDispersions( pasillaExons )
        pasillaExons <- fitDispersionFunction( pasillaExons )
        pasillaExons <- testForDEU( pasillaExons )
     
## End(Not run)
[Package DEXSeq version 1.8.0 Index]