I am doing EWAS analysis to get DMP, DMR and Enrichment pathway analysis. However, most packages do not support EPIC v2. I was so lucky to find some codes to get DMP, but still, now, I did not find a way to get Differentially methylated region (DMR). Is there a way to get it? I am trying to understand how these packages calculate DMR but it is confusing.
Thank you James for your insight, I did this step earlier in the beginning of the analysis, but I am encountering a challenge when specifying parameters in the cpg.annotate function for DMR (Differentially Methylated Regions) analysis.
The goal is to include the array type (IlluminaHumanMethylationEPICv2) and the annotation (20a1.hg38) in my analysis. However, I am unsure if I'm specifying the parameters correctly in the cpg.annotate function, especially in relation to the design and contrast matrices.
This the code in the minfi pipeline
I adjusting the code for EPIC v2 as following, still does not work. seems to me to get DMR is not possible we have to wait for the package to be updated. I am getting error message
"
You want to make sure that you already have a
GenomicRatioSet
that you pass intocpg.annotate
.You don't have to specify the 'what' or 'datatype' arguments (see
?cpg.annotate
).Hi, I was having similar issue but using your suggested code resulted in following (new problem)
any solution plz?
Yes. Did you read the error message? The row.names of your matrix have to be Illumina IDs that match the array you are using.
Hello, I'm facing the same problem and I'm unable to solve it. Did you found the way of solving it? Thanks in advanced, it is getting quite complicated to adapt EPIC pipeline to EPIC V2, I will really appreciate any help.
There is this code in
cpg.annotate
And if you are loading the 'IlluminaHumanMethylationEPICanno.ilm10b4.hg19' package and getting an error that your EPICV2 row names don't match the IlluminaHumanMethylation450k probe names, that's an indication that you have told
cpg.annotate
that you are using a 450k array instead of an EPICV2 array.Hello, DMRcate for EPICv2 is now in release, and there is also a tutorial, see How to get DMR for Infinium methylation EPIC v2
Cheers, Tim