plotMA-methods {DEXSeq} | R Documentation |
This function generates an MA plot.
## 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, ... )
object |
Either a |
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 |
## 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)