Documentation - Appropriate Normalization

[mehrankr]

Thanks a lot for the very promising algorithm of bump hunter and the R package.

I am trying to use the bumphunter package and after consulting the user guide and the manuscript, I am confused on whether I should perform any sort of normalization before feeding the beta values as Y into the bumphunter function or not.

My confusion is due to the fact that instead of using a usual bed or bedgraph as input, the documentation is filled with unnecessary chunks of code for simulating multiple vectors of data. This makes it very inefficient for someone who wants to use the package to try to understand what parts of the documentation is just unnecessary simulations and which parts are necessary preprocessing of methylation estimates.

Cheers
Mehran