R: Perform complete differential exon usage analysis

doCompleteDEUAnalysis {DEXSeq}

R Documentation

Perform complete differential exon usage analysis

Description

This function performs a complete differential exon usage analysis, calling all the necessary functions and returning an ExonCountSet object with p values, adjusted p values and fold change estimates.

Usage

doCompleteDEUAnalysis( ecs, 
     formula0 = ~ sample + exon, 
     formula1 = ~ sample + exon + condition:exon, 
     minCount = 10,
     nCores = 1, 
     path = NULL, 
     FDR = 0.1, 
     fitExpToVar = "condition", 
     color = NULL, 
     color.samples = NULL )

Arguments

`ecs`	An ExonCountSet object.
`formula0`	Formula for the reduced (null) model, to be passed to `testForDEU`; see there for details.
`formula1`	Formula for the full model, to be passed to `estimateDispersions` and `testForDEU`; see there for details.
`minCount`	Exons with less than ‘minCount’ reads (summed over all samples) are excluded from the test. See `estimateDispersions` for details.
`nCores`	Number of CPU cores to be used when running `estimateDispersions` and `testForDEU`. Load the “parallel” package beforehands if you want to use more than one core.
`path`	A file system path to the directory into which the HTML report generated by `DEXSeqHTML` shoudl be written. If NULL, no report will be created.
`FDR`	Argument passed on to `DEXSeqHTML`; see there for details.
`fitExpToVar`	Argument passed on to `DEXSeqHTML`; see there for details.
`color`	Argument passed on to `DEXSeqHTML`; see there for details.
`color.samples`	Argument passed on to `DEXSeqHTML`; see there for details.

Value

An object of class ExonCountSet.

Examples

data("pasillaExons", package="pasilla")
pasillaExons <- doCompleteDEUAnalysis( pasillaExons, 
   formula0 = ~ sample + type * exon, 
   formula1 = ~ sample + type * exon + condition * exon )

[Package DEXSeq version 1.8.0 Index]