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)