plotMA-methods {DEXSeq} | R Documentation

## Generate an MA plot

### Description

This function generates an MA plot.

### Usage

      ## S4 method for signature 'DEXSeqDataSet'
    plotMA( object, alpha=0.1, ylim=c(-2, 2), foldChangeColumn=NULL, ... )

      ## S4 method for signature 'DEXSeqResults'
    plotMA( object, alpha=0.1, ylim=c(-2, 2), foldChangeColumn=NULL, ... )

### Arguments

`object` | Either a `DEXSeqDataSeq` or a `DEXSeqResults`.
`alpha` | the false discovery rate, i.e., threshold to the adjusted p values, to be used to colour the dots
`ylim` | y-limits of the plot
`foldChangeColumn` | Name of the column containing the fold changes to plot. If NULL, the first fold change column from the object will be taken.
`...` | Further parameters to be passed through to `plot`.

### Examples

     ## Not run:
        data(pasillaDEXSeqDataSet, package="pasilla")
        dxd <- estimateSizeFactors( dxd )
        dxd <- estimateDispersions( dxd )
        dxd <- testForDEU( dxd )
        dxd <- estimateExonFoldChanges( dxd )
        dxr <- DEXSeqResults( dxd )

        plotMA( dxr )

        plotMA( dxd )

    ## End(Not run)

[Package DEXSeq version 1.38.0 Index]