Hello,
I am interested in using your tool for finding significant CpG island between case and control. Can I use customized region for finding significant DMR? I mean changing combined.csv to customized region file like CpG island. If it is possible, what's the format (which column combined.csv needs to contain) should I create.
Thanks for your help!
Honchkrow
Thanks for the question. Yes, you can filter your csv file before running findDMRs.r. To select only regions overlapping a reference, I would recommend a tool such as bedtools.
The format of the input file for findDMRs.r is given under the description of the -i <input> argument here.
Hello, I am interested in using your tool for finding significant CpG island between case and control. Can I use customized region for finding significant DMR? I mean changing combined.csv to customized region file like CpG island. If it is possible, what's the format (which column combined.csv needs to contain) should I create. Thanks for your help! Honchkrow