getAnnot: Get CpG annotation

In reese3928/methylGO: Gene Set Analysis Using the Outcome of Differential Methylation

Description

This function gets CpG IDs and their corresponding gene symbols.

Usage

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

Arguments

array.type

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

group

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.

Details

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

Value

A data frame contains CpG IDs and gene symbols.

References

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, https://bitbucket.com/kasperdanielhansen/Illumina_EPIC.

Phipson B, Maksimovic J and Oshlack A (2015). “missMethyl: an R package for analysing methylation data from Illuminas HumanMethylation450 platform.” Bioinformatics, pp. btv560.

reese3928/methylGO documentation built on May 8, 2021, 8:08 p.m.