Hi everyone!

I am unsure what is causing my DMRfinder R program to not work. I did not use the DMRfinder pileup step (using bismark) because I wanted to test my own pileups. Therefore, I reformatted existing bedgraph files to have the following format:

I then got the following combined bed file from running two bed samples:

Here is the command line I ran while I was cd'd into the folder that all these files are/would be located:

Rscript /pathtocode/DMRfinderinst/DMRfinder-master/findDMRs.r -i both.combined.bed -o DMRsFound.csv Methyldackelbiscuittest Methyldackelbsmaptest -n Methyldackelbiscuittest,Methyldackelbsmaptest -d 0 -p 1

My output was as follows:

There were 23 warnings (use warnings() to see them)
Error in if (substr(level[i], 1, 3) == "chr") { :
  argument is of length zero
Execution halted

I admit I am not proficient at R myself to troubleshoot this issue. At first I thought this was because some of my chr outputs were formatted as satellite chromosomes, but this was after I subsetted out the non chr 1:22, chrX, chrY chromosomes.

Any insight would be helpful, thank you!