Unpaired Data with DMRMark

Question

[lizlitkowski]

I am trying to find differentially methylated regions using the R package DMRMark. My data is unpaired data between controls and cases and I went back to the example in the DMRMark Reference Manual to make sure I had the steps. In the code below, the first 5 lines are directly from the manual.

I was trying to use the output from the 'reformData' function as the input to the 'DMRMark' function but I tried it 3 ways and I get errors. I expect the first option to work but it gives the error that I have 'NA's in my data. The reformData function creates the 'NA's so that error was a particular surprise.

Any thoughts on what I am doing wrong here?

# The case with One more sample from Tumour group
# The second Tumour sample is the extra one
mv2 <- matrix(1:25,5)
mv2[,2] <- mv2[,2] + 5
patient <- factor(c(1,3,1:3))
type = c(rep("Normal",2),rep("Tumour",3))
pd <- model.matrix(~patient + type + 0)
exmpl = reformData(mv2, pd)
L = c(300,2578,608,362,48)
set.seed(13)
starting = 1 
par <- DMRMark(exmpl, L, starting)
par <- DMRMark(exmpl, L, starting, pd = pd)
par <- DMRMark(mv2, L, starting, pd = pd)