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. Author manuscript; available in PMC: 2011 Dec 2.
Published in final edited form as: Nat Protoc. 2011 Jun 2;6(6):870–895. doi: 10.1038/nprot.2011.328 
> RTb = subset(RT, RT$CHR == “chr1”)
 
# Create a subset of timing values in chromosome 1
 
> par(mar=c(3.1,4.1,1,1),mfrow=c(2,1))
 
# Set plot margins; include two rows in layout
 
> plot(RTb[,1]~RTb$POSITION,pch=19,cex=0.2,col=“grey”,ylim=c(−3,3))
 
# Plot replicate 1
 
> plot(RTb[,2]~RTb$POSITION,pch=19,cex=0.2,col=“grey”,ylim=c(−3,3))
 
# Plot replicate 2