plotMA: Generate an MA plot

In DEXSeq: Inference of differential exon usage in RNA-Seq

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)

DEXSeq documentation built on Nov. 8, 2020, 5:11 p.m.