A question about the EPIC_10b4_Gene_3_200.rds and EPIC_10b4_InterGene_3_200.rds files

Question

A question about the EPIC_10b4_Gene_3_200.rds and EPIC_10b4_InterGene_3_200.rds files

Closed this issue 4 months ago · 2 comments

Hello Gabriel, I couldn't find the code for generating the EPIC_10b4_Gene_3_200.rds and EPIC_10b4_InterGene_3_200.rds files. Are there any criteria for defining gene and intergenic methylation regions? Thanks!

Best regards
Qianhui

Answer 1 · 2024-04-17T13:30:46.000Z

Hi Qianhui - these clusters were created using the WriteClosebyAllRegions() function in the package. I believe genic regions are those probes with gene names in the Illumina manifest, intergenic regions are those probes without gene names in UCSC_RefGene_Name
-Lily

Answer 2 · 2024-05-07T07:59:47.000Z

Hi Qianhui - these clusters were created using the WriteClosebyAllRegions() function in the package. I believe genic regions are those probes with gene names in the Illumina manifest, intergenic regions are those probes without gene names in UCSC_RefGene_Name -Lily

Hi Lily, thank you so much.