So I've been given a JMP file containing methylation percentage data for a few subjects. The file is organized by columns, containing the chromosome number, position on chromosome, and percentage of methylation for that location for each subject (15 subjects total).
I tried going over a few bioconductor packages for R as well as different software for methylation analysis, but found no one that can handle this kind of data. The purpose is to run an analysis (similar to a gwsa using Plink, for exmaple) in order to find differences in methylations between the study groups.
Any advice on either how to organize the file to a more proper file format or which software will be appropriate for the situation?