getAnnot: Get CpG annotation

Description Usage Arguments Details Value References

View source: R/getAnnot.R


This function gets CpG IDs and their corresponding gene symbols.


getAnnot(array.type, group = "all")



A string. Either "450K" or "EPIC". Default is "450K".


A string. "all", "body", "promoter1" or "promoter2". Default is "all". If group = "body", only CpGs on gene body will be pulled out. If group = "promoter1" or group = "promoter2", only CpGs on promoters will be pulled out. Here is the definition of "body", "promoter1" and "promoter2" according to the annotation in IlluminaHumanMethylation450kanno.ilmn12.hg19 or IlluminaHumanMethylationEPICanno.ilm10b4.hg19.

  • body: CpGs whose gene group correspond to "Body" or "1stExon"

  • promoter1: CpGs whose gene group correspond to "TSS1500" or "TSS200"

  • promoter2: CpGs whose gene group correspond to "TSS1500", "TSS200", "1stExon", or "5'UTR".

If group = "all", all CpGs will be pulled out.


The implementation of the function is modified from .flattenAnn function in missMethyl package.


A data frame contains CpG IDs and gene symbols.


Hansen KD (2016). IlluminaHumanMethylation450kanno.ilmn12.hg19: Annotation for Illumina's 450k methylation arrays. R package version 0.6.0.

Hansen KD (2017). IlluminaHumanMethylationEPICanno.ilm10b4.hg19: Annotation for Illumina's EPIC methylation arrays. R package version 0.6.0,

Phipson B, Maksimovic J and Oshlack A (2015). <e2><80><9c>missMethyl: an R package for analysing methylation data from Illuminas HumanMethylation450 platform.<e2><80><9d> Bioinformatics, pp. btv560.

methylGSA documentation built on Nov. 8, 2020, 8:29 p.m.