Generate an MA plot — plotMA-methods • DEXSeq

This function generates an MA plot.

Usage

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

  # S4 method for class '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

 if (FALSE) { # \dontrun{
    data(pasillaDEXSeqDataSet, package="pasilla")
    dxd <- estimateSizeFactors( dxd )
    dxd <- estimateDispersions( dxd )
    dxd <- testForDEU( dxd )
    dxd <- estimateExonFoldChanges( dxd )
    dxr <- DEXSeqResults( dxd )

    plotMA( dxr )

    plotMA( dxd )
    
 } # }