Skip to contents

Annotate CpG Sites with Gene Information

annotate_cpg_sites.Rd

This function annotates a vector of CpG site probe IDs by retrieving corresponding gene names from the Illumina 450k annotation package. It returns a data frame with the original CpG sites and their associated gene names.

Usage

annotate_cpg_sites(
  cpg_vector,
  annotation_package = "IlluminaHumanMethylation450kanno.ilmn12.hg19"
)

Arguments

cpg_vector

A character vector of CpG site probe IDs to be annotated.

annotation_package

A character string specifying the Illumina annotation package to use. It can be one of the following:

  • "IlluminaHumanMethylation450kanno.ilmn12.hg19" (default)

  • "IlluminaHumanMethylationEPICanno.ilm10b4.hg19"

Value

A data frame with two columns:

  • CpG_Site: The original CpG site probe IDs.

  • Gene: The associated gene names. NA if no gene annotation is found.

Examples

if (FALSE) { # \dontrun{
library(IlluminaHumanMethylation450kanno.ilmn12.hg19)
library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19)
# Example CpG probe IDs
cpg_ids <- c("cg00000029", "cg00000108", "cg00000109")
# Annotate CpG sites
annotate_cpg_sites(cpg_ids, "IlluminaHumanMethylation450kanno.ilmn12.hg19")
} # }