[Bioc-devel] Manifest and annotation packages for EPIC methylation array v2.0

[Zuguang Gu]

Hi Bioc-devel,

I recently analyzed a methylation array dataset which is from EPIC array
v2.0 (
https://www.illumina.com/products/by-type/microarray-kits/infinium-methylation-epic.html)
and currently there is no manifest nor annotation packages for that one.
The available packages on Bioconductor are only for EPIC array v1.0:

- IlluminaHumanMethylationEPICmanifest
- IlluminaHumanMethylationEPICanno.ilm10b4.hg19

And it is not proper to use the v1 packages for the v2 data.

I've built a manifest package and an annotation package for the EPIC array
v2.0. They are available at:

https://github.com/jokergoo/IlluminaHumanMethylationEPICv2manifest
https://github.com/jokergoo/IlluminaHumanMethylationEPICv2anno.20a1.hg38

Basically they are built with the scripts in the original v1 packages, with
small adjustment. The scripts for building the two packages are also
included in the two packages.

The two v2 packages can be seamlessly integrated into the minfi analysis.

I also did some simple comparisons between v1 and v2 (
https://jokergoo.github.io/IlluminaHumanMethylationEPICv2manifest/articles/IlluminaHumanMethylationEPICv2manifest.html
).

Since the v1 packages were developed by the bioc core members, I want to
ask is there any plan to support the EPIC v2 array officially? If there is
no such plan, can I submit the two packages to bioc? If I can, then I will
have some additional questions regarding how to pass BiocCheck (e.g. file
size, lazy loading, ...). But that will be in another email.

Best,
Zuguang

	[[alternative HTML version deleted]]