R: Generate an MA plot

plotMA-methods {DEXSeq}

R Documentation

Generate an MA plot

Description

This function generates an MA plot.

Usage


## S4 method for signature 'data.frame'
plotMA( object, ylim = NULL,
  colNonSig = "gray32", colSig = "red3", colLine = "#ff000080",
  log = "x", cex=0.45, xlab="mean expression", ylab="log fold change", ... )

## S4 method for signature 'ExonCountSet'
plotMA( object, FDR = 0.1, ... )

Arguments

`object`	either an ExonCountSet or a data.frame. If object is a data.frame, it must contain three columns, the first containing the mean expression values (for the x axis), the second the log fold change (for the y axis) and the third must be a logical vector indicating significance (for the coloring of the dots)
`FDR`	the false discovery rate, i.e., threshold to the adjusted p values, to be used to colour the dots
`ylim`	The limits for the y axis. If missing, an attenpt is made to choose a sensible value. Dots exceeding the limits will be displayed as triangles at the limits, pointing outwards.
`colNonSig`	color to use for non-significant data points
`colSig`	color to use for significant data points
`colLine`	color to use for the horizontal zero line
`log`	which axis should be logarithmic; will be passed to `plot`
`cex`	The `cex` parameter for `plot`.
`xlab`	The x axis label.
`ylab`	The y axis label.
`...`	Further parameters to be passed through to `plot`.

Examples

     ## Not run: 
        data("pasillaExons", package="pasilla")
        pasillaExons <- estimateSizeFactors( pasillaExons )
        pasillaExons <- estimateDispersions( pasillaExons )
        pasillaExons <- fitDispersionFunction( pasillaExons )
        pasillaExons <- testForDEU( pasillaExons )
        pasillaExons <- estimatelog2FoldChanges( pasillaExons )
        plotMA( pasillaExons )
     
## End(Not run)

[Package DEXSeq version 1.8.0 Index]