Customizing Annotation Packages for EPICv2

[BigGoose3]

Hello,

I have some methlyation EPICv2 data that I am trying to perform differential methylation regional (DMR) analysis on, and am having some trouble using the customized packages (specifically the v2 annotation and manifest from jokergoo). I was able to analyze a majority of it using minfi (preprocessing, PCA, differential probes, DNA methylation age analysis), but cannot use DMRcate with these customizable packages to map these probes to the genome. Is this something that Shinyepico can do, or is this still in development also?

Thank you!!

[omorante]

Hello,

I understand that you have used shinyepico to analyze EPICv2 data, using annotation and manifest from jokergoo? Since this feature is still on-going, it would be useful if you can share any issues that you faced using it.

The ideal solution would be submitting the new annotation packages to Bioconductor and autodetecting the array type in shinyepico. Unfortunately, minfi does not seem to be updated.

Regarding DMR analysis, shinyepico currently supports only mCSEA package. I would need to check if some update is on-going, but currently it does not support the new EPICv2 array. I could also generate a new annotation to support it, but it would require some time.

I would like to update shinyepico to fully support EPICv2 when I have some time, but in the meantime I just added a workaround to be able to select any custom annotation.

[BigGoose3]

Hello, Thank you for your response! I apologize, my wording was likely not very clear. I was able to analyze a majority of my data using the minfi workflow, not using shinyepico. With the jokergoo packages, I was able to obtain PCA plots, differentially methylated probes, and DNAm Age scores, but am having some trouble finding differentially methylated regions with the jokergoo packages. On shinyepico, I was only able to pre-process the data and obtain normalization and PCA results, but not DMP or DMRs.

Basically, I was wondering if you had any success in DMR analysis with EPICv2 data, but it does not sound like that is the case yet. I will be also doing some digging to see if there are any updates in the works or if there is an accessible workaround. Thank you!

[omorante]

Yes, unfortunately the mCSEA method integrated in shinyepico does not work with EPICv2 yet. I will work to have shinyepico with full functionality for EPICv2.

With the functions already implemented, you should be able to obtain DMPs using shinyepico in EPICv2, selecting the custom annotation option and the proper annotation package

El lun, 16 oct 2023 a las 20:42, biggoose3 @.***>) escribió:

Hello, Thank you for your response! I apologize, my wording was likely not very clear. I was able to analyze a majority of my data using the minfi workflow, not using shinyepico. With the jokergoo packages, I was able to obtain PCA plots, differentially methylated probes, and DNAm Age scores, but am having some trouble finding differentially methylated regions with the jokergoo packages. On shinyepico, I was only able to pre-process the data and obtain normalization and PCA results, but not DMP or DMRs.

Basically, I was wondering if you had any success in DMR analysis with EPICv2 data, but it does not sound like that is the case yet. I will be also doing some digging to see if there are any updates in the works or if there is an accessible workaround. Thank you!

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