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

In REMP: Repetitive Element Methylation Prediction

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

REMP documentation built on Nov. 8, 2020, 8:05 p.m.