getGM12878: Get methylation data of HapMap LCL sample GM12878 profiled by...

In YinanZheng/REMP: Repetitive Element Methylation Prediction

Get methylation data of HapMap LCL sample GM12878 profiled by Illumina 450k array or EPIC array

Description

getGM12878 is used to obtain public available methylation profiling data of HapMap LCL sample GM12878.

Usage

getGM12878(arrayType = c("450k", "EPIC"), mapGenome = FALSE)

Arguments

arrayType	Illumina methylation array type. Currently "450k" and "EPIC" are supported. Default = "450k".
mapGenome	Logical parameter. If TRUE, function will return a GenomicRatioSet object instead of a link{RatioSet} object.

Details

Illumina 450k data were sourced and curated from ENCODE http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450Gm12878SitesRep1.bed.gz. Illumina EPIC data were obtained from data package minfiDataEPIC.

Value

A RatioSet or GenomicRatioSet containing beta value and M value of the methylation data.

Examples

## Not run: 
# Get GM12878 methylation data (450k array)
if (!exists("GM12878_450k")) GM12878_450k <- getGM12878("450k")
GM12878_450k

## End(Not run)

# Get GM12878 methylation data (EPIC array)
if (!exists("GM12878_EPIC")) GM12878_EPIC <- getGM12878("EPIC")
GM12878_EPIC

YinanZheng/REMP documentation built on May 14, 2022, 5:58 p.m.