<p>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?</p>
<p>Through research I have stumbled upon epicopy (<a href="https://github.com/sean-cho/Epicopy/blob/master/vignettes/Epicopy.Rmd" rel="nofollow noreferrer">https://github.com/sean-cho/Epicopy/blob/master/vignettes/Epicopy.Rmd</a>), but I'm uncertain whether this is the best package for this problem.</p>
<p>Cheers,
GB</p>

CC BY-SA 4.0
2020-10-29T01:45:19.553Z
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.
M__
CC BY-SA 4.0
2020-10-29T14:24:03.863Z
I am not too familiar with this, but conumee (https://bioconductor.org/packages/release/bioc/vignettes/conumee/inst/doc/conumee.html) seems promising
burger
<r><methylation><copy-number>
How to use EPIC DNAm files (.idat) to infer copy number alteration
# How to use EPIC DNAm files (.idat) to infer copy number alteration

(Asked by: username_0 on 2020-10-27)

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

**Tags:** r, methylation, copy-number
> **Comments:**
> **username_1**: 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.  
> **username_2**: I am not too familiar with this, but conumee (https://bioconductor.org/packages/release/bioc/vignettes/conumee/inst/doc/conumee.html) seems promising  

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