3.4 years ago by
Max Planck Institute for molecular Genetics, Berlin, Germany
I recently developed qsea, an alternative package for the analysis of enrichment based methylation data, which is in the currently in the devel-branch of Bioconductor. The package is based on the ideas of MEDIPS, but extends the functionality and facilitates the usage. The focus is on estimating absolute methylation levels, but it also includes a more flexible function to estimate pattern densities, just as you suggested: the addPatternDensity function has a parameter "fixed", that allows for flexible patterns. This is however not the only change within this function. But even if you chose to extend MEDIPS, I'd suggest having a look at the function, as there are pitfalls with this approach, mainly due to the Ns in the reference, that unintentionally matches any character in the pattern.