R: Test for Differential Exon Usage.

testForDEU {DEXSeq}

R Documentation

Test for Differential Exon Usage.

Description

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

Usage

testForDEU(ecs, formula0=NULL, formula1=NULL, nCores=1, quiet=FALSE, file="")

Arguments

`ecs`	An ExonCountSet object.
`formula0`	Formula for the null model to be used in the GLM fit. If no formula is given, the default `count ~ sample + exon + condition` is used. See below for details
`formula1`	Formula for the full model to be used in the GLM fit. If no formula is given, the default `count ~ sample + exon + condition *I (exon==exonID)` is used. See below for details.
`nCores`	Number of CPUcores to be used to estimate the dispersions. The `multicore` package must be loaded to use more than 1 core.
`quiet`	If TRUE, no progress report is shown. In case the session is not an interactive session and progress report is wanted. Change the name of the file.
`file`	A file name to write the progress reports. If file="", output will be written in the standard output connection.

Details

The terms in the formulas must be columns of design(ecs). In addition, in formula1, the variable exonID is set to the ID of the currently tested exon counting bin.

See testGeneForDEU, which is called for each gene, for further details.

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 1.0.2 Index]