plotMA {edgeR}R Documentation

MA-like plot for deDGEList objects

Description

Plots M (log-abundance ratio) against A (log-average abundance) for two groups. A smear of points is shown on the left side for those genes with 0 counts in 1 of the 2 classes.

Usage

 
plotMA(object,pair=c(1,2),xlab="A",ylab="M",ylim=NULL,pch=19,eps=0,smearOffset=0,...)

Arguments

object deDGEList object, as output from deDGE
pair pair of groups to be plotted; default plots groups 1 and 2
xlab x-axis label
ylab y-axis label
ylim limits on y-axis, if left at NULL, scaled to be symmetric about 0
pch plot character
eps offset to plot in the log-ratios (i.e. log( [p1+eps]/[p2+eps] )
smearOffset offest (to the left of the minimum A value) to plot the smear of 0-in-1-group values
... further arguments to the plot command

Value

A plot to the current device

Author(s)

Mark Robinson, Davis McCarthy

See Also

deDGE

Examples

# generate raw data from NB, create list object
y<-matrix(rnbinom(20,size=1,mu=10),nrow=5)
d<-DGEList(data=y,group=rep(1:2,each=2),lib.size=rep(c(1000:1001),2))

# find alpha and call main procedure to find differences
alpha<-alpha.approxeb(d)
ms<-deDGE(d,alpha=alpha$alpha)

# plot it
plotMA(ms)

[Package edgeR version 1.2.4 Index]