plotMA {edgeR} | R Documentation |
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.
plotMA(object,pair=c(1,2),xlab="A",ylab="M",ylim=NULL,pch=19,eps=0,smearOffset=0,...)
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 |
A plot to the current device
Mark Robinson, Davis McCarthy
deDGE
# 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)