I have access to EPIC DNA methylation profiles from approximately 40 samples. I want to use these .idat files in order to predict copy number alterations within specific promoter regions of interest. Can you recommend any R packages that could perform this task?

Through research I have stumbled upon epicopy (https://github.com/sean-cho/Epicopy/blob/master/vignettes/Epicopy.Rmd), but I'm uncertain whether this is the best package for this problem.

Cheers, GB

  • $\begingroup$ This is a good question and very interesting area of investigation. The package you sourced looks okay from my 'outside the field' perspective, but I understand your concerns. $\endgroup$
    – M__
    Oct 29 '20 at 1:45
  • $\begingroup$ I am not too familiar with this, but conumee (bioconductor.org/packages/release/bioc/vignettes/conumee/inst/…) seems promising $\endgroup$
    – burger
    Oct 29 '20 at 14:24

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