plotMA: MA-plot from base means and log fold changes

In aghozlane/DESeq2shaman: Differential gene expression analysis based on the negative binomial distribution

Description

A simple helper function that makes a so-called "MA-plot", i.e. a scatter plot of log2 fold changes (on the y-axis) versus the mean of normalized counts (on the x-axis).

Usage

## S4 method for signature 'DESeqResults'
plotMA(object, alpha, main, ylim, ...)
## S4 method for signature 'DESeqDataSet'
plotMA(object, alpha, main, ylim, ...)

## S4 method for signature 'DESeqDataSet'
plotMA(object, alpha = 0.1, main = "", ylim, ...)

## S4 method for signature 'DESeqResults'
plotMA(object, alpha = 0.1, main = "", ylim, ...)

Arguments

object	a DESeqResults object produced by results; or a DESeqDataSet processed by DESeq, or the individual functions nbinomWaldTest or nbinomLRT
alpha	the significance level for thresholding adjusted p-values
main	optional title for the plot
ylim	optional y limits
...	further arguments passed to plotMA if object is DESeqResults or to results if object is DESeqDataSet

Details

This function is essentially two lines of code: building a data.frame and passing this to the plotMA method for data.frame from the geneplotter package. The code of this function can be seen with: getMethod("plotMA","DESeqDataSet") If users wish to modify the graphical parameters of the plot, it is recommended to build the data.frame in the same manner and call plotMA.

Value

A trellis object.

Author(s)

Michael Love

Examples

dds <- makeExampleDESeqDataSet()
dds <- DESeq(dds)
plotMA(dds)
res <- results(dds)
plotMA(res)

aghozlane/DESeq2shaman documentation built on Nov. 1, 2019, 9:01 p.m.