mQTL mapping in bisulfite sequencing studies by fitting a binomial mixed model, incorporating allelic-specific methylation pattern.
It is easy to install the development version of MethylQTL package using the 'devtools' package.
The main function is image. You can find the instructions and an example by '?image'.
All the results from all methods used in the PMR-Egger paper can be reproduced at https://github.com/3211895/IMAGEreproduce