DEXSeq (version 1.18.4)

plotMA-methods: Generate an MA plot

Description

This function generates an MA plot.

Usage

"plotMA"( object, alpha=0.1, ylim=c(-2, 2), foldChangeColumn=NULL, ... )
  "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)