Change the genomic.features parameters to custom-made features in goregion function

[AphroditeLibra]

Hi
I try to analyze genomic regions analysis with goregion function.

I want to change the genomic.features parameters to my own custom-made features (e.g. Island, N_shelf, etc.) from the column “Relation to UCSC CpG Island” in the annotation file. I tried to include these features in the code but it didn’t work. How do I perform goregion analysis with these features?

Your help would be highly appreciated.

Best regards

[bphipson]

The way that goregion works is to extract the CpGs underlying the regions and then use the gometh statistical framework. At the moment we only allow subsetting to the column "UCSC_RefGene_Group" and you would need to manually subset the CpGs underlying the regions to allow for custom-made features from other columns of the annotation prior to running gometh.

[JovMaksimovic]

Another way to restrict your regions based on your custom-made features is to overlap your custom-feature Granges object with your with your DMRs Granges. Then you can use the resulting Granges as input to GOregion.