Is your feature request related to a problem? Please describe.
In order to use the hypermr command to find hypermethylated regions in plant genomes, I need to run the sym command on my CpG sites or else I get an error. However, running the sym command on my counts data removes non-CpG sites, which are needed to find hypermethylated regions. I see you recommend separating by cytosine context, but I'd appreciate being able to analyse all contexts together in one go.
Describe the solution you'd like
Have an option on the sym command to keep non-CpG sites after CpG processing.
Describe alternatives you've considered
I can simply create non-CpG and CpG versions of my counts files using grep, and then put them back together after running sym on the CpG files, but it'd be more straightforward if dnmtools could do it inherently.
Thank you.
Is your feature request related to a problem? Please describe.
In order to use the hypermr command to find hypermethylated regions in plant genomes, I need to run the sym command on my CpG sites or else I get an error. However, running the sym command on my counts data removes non-CpG sites, which are needed to find hypermethylated regions. I see you recommend separating by cytosine context, but I'd appreciate being able to analyse all contexts together in one go.
Describe the solution you'd like
Have an option on the sym command to keep non-CpG sites after CpG processing.
Describe alternatives you've considered
I can simply create non-CpG and CpG versions of my counts files using grep, and then put them back together after running sym on the CpG files, but it'd be more straightforward if dnmtools could do it inherently.
Thank you.